Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional Studies of [FeFe] Hydrogenase Maturation in an Escherichia coli Biosynthetic System

ABSTRACT Maturation of [FeFe] hydrogenases requires the biosynthesis and insertion of the catalytic iron-sulfur cluster, the H cluster. Two radical S-adenosylmethionine (SAM) proteins proposed to function in H cluster biosynthesis, HydEF and HydG, were recently identified in the hydEF-1 mutant of the green alga Chlamydomonas reinhardtii (M. C. Posewitz, P. W. King, S. L. Smolinski, L. Zhang, M. Seibert, and M. L. Ghirardi, J. Biol. Chem. 279:25711-25720, 2004). Previous efforts to study [FeFe] hydrogenase maturation in Escherichia coli by coexpression of C. reinhardtii HydEF and HydG and the HydA1 [FeFe] hydrogenase were hindered by instability of the hydEF and hydG expression clones. A more stable [FeFe] hydrogenase expression system has been achieved in E. coli by cloning and coexpression of hydE, hydF, and hydG from the bacterium Clostridium acetobutylicum. Coexpression of the C. acetobutylicum maturation proteins with various algal and bacterial [FeFe] hydrogenases in E. coli resulted in purified enzymes with specific activities that were similar to those of the enzymes purified from native sources. In the case of structurally complex [FeFe] hydrogenases, maturation of the catalytic sites could occur in the absence of an accessory iron-sulfur cluster domain. Initial investigations of the structure and function of the maturation proteins HydE, HydF, and HydG showed that the highly conserved radical-SAM domains of both HydE and HydG and the GTPase domain of HydF were essential for achieving biosynthesis of active [FeFe] hydrogenases. Together, these results demonstrate that the catalytic domain and a functionally complete set of Hyd maturation proteins are fundamental to achieving biosynthesis of catalytic [FeFe] hydrogenases.
Scales to measure dimensions of hallucinations and delusions: the psychotic symptom rating scales (PSYRATS)

Background. Scales to measure the severity of different dimensions of auditory hallucinations and delusions are few. Biochemical and psychological treatments target dimensions of symptoms and valid and reliable measures are necessary to measure these. Method. The inter-rater reliability and validity of the Psychotic Symptom Rating Scales (PSYRATS: auditory hallucination subscale and delusions subscale), which measure several dimensions of auditory hallucinations and delusions were examined in this study. Results. The two scales were found to have excellent inter-rater reliability. Their validity as compared with the KGV scale (Krawiecka et al. 1977) was explored. Conclusions. It is concluded that the PSYRATS are useful assessment instruments and can complement existing measures.
Lowering of cytoplasmic pH is essential for growth of Streptococcus faecalis at high pH

The growth of Streptococcus faecalis at high pH was significantly stimulated by carbonate. In the absence of added carbonate the cells were unable to grow at a pH above 9.5, but in media containing 50 mM HCO3- they grew even at pH 10.5. Both rate and yield of growth at pH 9.5 were significantly stimulated by as little as 5 mM carbonate. The cytoplasmic pH in growing cells was maintained at about 7.8 to 8.2, whereas the medium pH ranged from 8.4 to 9.5. Nigericin and gramicidin D, ionophores which conduct protons, blocked growth at pH 9.5 but not at pH 7.5. These results indicate that lowering of the cytoplasmic pH is essential for the growth of this organism at high pH.
Are thrombocytes and platelets true phagocytes?

Thrombocytes and platelets, beyond their primary function in hemostasis, seem to play an active role in inflammation. As regards their phagocytic ability, the results to date are confusing, incomplete, and somewhat contradictory. Whereas the interaction of avian thrombocytes or mammalian platelets with bacteria both in vitro and in vivo has received wide attention, almost no information exists on the topic in “lower” vertebrates. The aim of this work is to review the available information on the phagocytic properties of thrombocytes and platelets. Particular attention is payed to the ontogeny of these cells, the soluble factors involved in the inflammatory process derived from them, and their interaction with particulate material, mainly with bacteria. Microsc. Res. Tech. 57:491–497, 2002. © 2002 Wiley‐Liss, Inc.
GENETIC MODELLING OF CHILDHOOD SOCIAL DEVELOPMENT AND PERSONALITY IN TWINS AND SIBLINGS WITH SCHIZOPHRENIA


Background Abnormalities in early social development and personality are present in patients with schizophrenia and their unaffected relatives. This study aimed to establish the degree to which these childhood and adolescent developmental abnormalities are genetically determined. Method We used a combined twin and family study design (n=531) to assess childhood and adolescent social adjustment and schizotypal personality traits in 98 twin pairs (n=196) varying in their zygosity and concordance for schizophrenia and 156 sibling clusters (n=335) varying in their concordance for schizophrenia. Results Schizophrenia was significantly associated with childhood and adolescent deficits in social adjustment and personality, with additive genetic effects being the main source of these phenotypic correlations. Conclusions Abnormalities of social adjustment and personality are present in children and adolescents who later develop schizophrenia, reflecting the influence of common genetic risk.
Biology of Human Tumors Genomic Classi fi cation of Serous Ovarian Cancer with Adjacent Borderline Differentiates RAS Pathway and TP 53-Mutant Tumors and Identi fi es NRAS as an Oncogenic Driver

Purpose: Low-grade serous ovarian carcinomas (LGSC) are Ras pathway-mutated, TP53 wild-type, and frequently associated with borderline tumors. Patients with LGSCs respond poorly to platinumbased chemotherapy and may benefit from pathway-targeted agents. High-grade serous carcinomas (HGSC) are TP53-mutated and are thought to be rarely associated with borderline tumors. We sought to determine whether borderline histology associated with grade 2 or 3 carcinoma was an indicator of Ras mutation, and we explored the molecular relationship between coexisting invasive and borderline histologies. Experimental Design:We reviewed >1,200 patients and identified 102 serous carcinomas with adjacent borderline regions for analyses, including candidatemutation screening, copy number, and gene expression
Practice parameter: Evaluation of the child with global developmental delay

— Objective: To make evidence-based recommendations concerning the evaluation of the child with a nonprogres-sive global developmental delay. Methods: Relevant literature was reviewed, abstracted, and classified. Recommendations were based on a four-tiered scheme of evidence classification. Results: Global developmental delay is common and affects 1% to 3% of children. Given yields of about 1%, routine metabolic screening is not indicated in the initial evaluation of a child with global developmental delay. Because of the higher yield (3.5% to 10%), even in the absence of dysmorphic features or features suggestive of a specific syndrome, routine cytogenetic studies and molecular testing for the fragile X mutation are recommended. The diagnosis of Rett syndrome should be considered in girls with unexplained moderate to severe developmental delay. Additional genetic studies (e.g., subtelomeric chromosomal rearrangements) may also be considered in selected children. Evaluation of serum lead levels should be restricted to those children with identifiable risk factors for excessive lead exposure. Thyroid studies need not be undertaken (unless clinically indicated) if the child underwent newborn screening. An EEG is not recommended as part of the initial evaluation unless there are historical features suggestive of epilepsy or a specific epileptic syndrome. Routine neuroimaging, with MRI preferred to CT, is recommended particularly if abnormalities are found on physical examination. Because of the increased incidence of visual and auditory impairments, children with global developmental delay may undergo appropriate visual and audiometric assessment at the time of diagnosis. Conclusions: A specific etiology can be determined in the majority of children with global developmental delay. Certain routine screening tests are indicated and depending on history and examination findings, additional specific testing may be performed.
Development of a Linearly Polarized Cavity-Backed Antenna Using HMSIW Technique

In this letter, a novel scheme for linear polarized cavity-backed antennas is introduced. In this design, for the first time, half-mode substrate integrated waveguide (HMSIW) technique is used to create a radiating aperture rather than minimizing the structure. The proposed antenna has the advantages of compactness, low profile, light weight, low fabrication cost, and easy integration with planar circuits. It also can be easily implemented by using only a single layer of printed circuit board (PCB). The proposed antenna is numerically investigated using HFSS. A sample antenna is fabricated, and its radiation characteristics are measured. The radiation patterns of the proposed antenna are also calculated based on the aperture antennas theory. Good agreement among calculated, simulation, and measured results is observed. The measured results show that the proposed antenna has also the advantages of conventional cavity-backed antennas including high gain, low cross-polarization level (CPL), and high front-to-back ratio (FTBR).
Glycoprotein B from strain 17 of herpes simplex virus type I contains an invariant chain homologous sequence that binds to MHC class II molecules

Major histocompatibility complex class I (MHCI) molecules are major targets of virus evasion strategies because they introduce antigens from the biosynthesis pathway into the antigen‐processing and presentation pathways for immune recognition by CD8+ T cells. Little is known about viral strategies that interfere with the MHC class II (MHCII) antigen presentation pathway. We identified a six amino acid sequence from type I herpes simplex virus (HSV‐1) glycoprotein B (gB) that is identical to a sequence of human leucocyte antigen D (HLA‐D) ‐associated invariant chain (Ii). In addition, this gB sequence is adjacent to a highly conserved HLA‐DR1 binding motif. Both viral sequences together resemble the class II binding site of human Ii, consisting of a MHCII groove binding segment and a promiscuous binding site. We cloned gB from HSV‐1 strain 17 and demonstrate association of the virus envelope protein to three HLA‐DR allotypes. With chimeric Ii/gB fusion proteins we identified gB sequences that mediate promiscuous or allotype‐specific binding to the HLA‐DR peptide‐binding domain. Mutation of two Lys residues in the viral segment of Ii/gB abolished promiscuous binding to HLA‐DR heterodimers. The result indicates promiscuous binding of the virus sequence to HLA‐DR molecules and suggests a potential for HSV‐1 to manipulate antigen processing and presentation.
Infectivity and Arthritis Induction of Borrelia japonica on SCID Mice and Immune Competent Mice: Possible Role of Galactosylceramide Binding Activity on Initiation of Infection

We investigated the relationship between the binding activity to galactosylceramide (GalCer) and the arthritis induction activity of Borrelia japonica. The B. japonica strains maintained the ability to induce arthritis in inbred C3H/HeN and immunodeficient SCID mice, but the ability was lower than that of Borrelia burgdorferi sensu stricto virulent strain 297. Histopathological changes were restricted to the joints, and a marked effusion of polymorphonuclear neutrophils into the joint space was found. The binding activity of B. japonica strains to GalCer was lower than that of the virulent strain 297 but higher than that of the high‐passage strain 297. The lower infectivity and virulence of B. japonica may explain its lower binding ability to GalCer.
Observation of kinetic and structural scalings during slow coalescence of nanobubbles in an aqueous solution.

The addition of salt can induce the slow coalescence of nanobubbles (approximately 100 nm) in an aqueous solution of alpha-cyclodextrin (alpha-CD). A combination of static and dynamic laser light scattering was used to follow the coalescence. Our results reveal that its kinetic and structural properties follow some scaling laws; namely, the average size () of the nanobubbles is related to their average mass () and the coalescence time (t) as approximately (d(f)) and approximately t(gamma) with two salt-concentration-dependent scaling exponents (d(f) and gamma). For a lower sodium chloride concentration (C(NaCl) = 40 mM), gamma = 0.13 +/- 0.01 and d(f) = 1.71 +/- 0.02. The increase of C(NaCl) to 80 mM results in gamma = 0.32 +/- 0.01 and d(f) = 1.99 +/- 0.01. The whole process has two main stages: the aggregation and the coalescence. At the lower C(NaCl), the process essentially stops in the aggregation stage with some limited coalescence. At higher C(NaCl), coalescence occurs after the aggregation and results in large bubbles.
Cell-Like Entities: On the Boundary Between Non-Living and Living

Abstract : In the last few decades, scientists have learned how to manipulate the basic components of life, how to design biomolecular networks, how to evolve biomolecules with unique characteristics and how to direct and control cellular processes at the molecular level. Using this knowledge as a foundation, it is theoretically possible to conceive of designing biological constructs, which we refer to as cell-like entities (CLEs), that use custom engineered biological machinery to accomplish specified tasks. The practical challenge is: Can we fabricate biological constructs for specific purposes using the same principles and components found in natural biological systems? For example, can CLEs be designed to detect very low levels of specific chemicals and fluoresce to indicate their presence; can they be designed to synthesize functional chemicals on demand, or can they use engineered metabolic pathways to detoxify environmental pollutants? The building of CLEs that could accomplish these goals would result in fundamental breakthroughs in exploiting our understanding of cellular control systems and biochemical information processing. The concept of the CLE is based on understanding how the biochemical reactions network that we call a living cell functions, how is it controlled and what are the key processes and components that will provide unique functions when integrated. The goal is not to create a living organism, but to create a biological construct that utilizes the essence of living systems to provide a wide array of solutions to current technological and medical challenges.
Spontaneous molecular reactivation of herpes simplex virus type 1 latency in mice

Infection of the mouse trigeminal ganglia (TG) is the most commonly used model for the study of herpes simplex virus type 1 (HSV-1) latency. Its popularity is caused, at least in part, by the perception that latent infection can be studied in this system in the absence of spontaneous viral reactivation. However, this perception has never been rigorously tested. To carefully study this issue, the eyes of Swiss–Webster mice were inoculated with HSV-1 (KOS), and 37–47 days later the TG were dissected, serial-sectioned, and probed for HSV-1 ICP4, thymidine kinase, glycoprotein C, and latency-associated transcript RNA by in situ hybridization. Serial sections of additional latently infected TG were probed with HSV-1-specific polyclonal antisera. Analysis of thousands of probed sections revealed abundant expression of viral transcripts, viral protein, and viral DNA replication in about 1 neuron per 10 TG tested. These same neurons were surrounded by a focal white cell infiltrate, indicating the presence of an antigenic stimulus. We conclude that productive cycle viral genes are abundantly expressed in rare neurons of latently infected murine TG and that these events are promptly recognized by an active local immune response. In the absence of detectable infectious virus in these ganglia, we propose the term “spontaneous molecular reactivation” to describe this ongoing process.
Transcriptional Regulation of Neuronal Nicotinic Acetylcholine Receptor Genes

Nicotinic acetylcholine receptors constitute a multigene family (α2–α9, β2–β4) expressed in discrete temporal and spatial patterns within the nervous system. The receptors are critical for proper signal transmission between neurons and their targets. The molecular mechanisms underlying receptor gene expression have not been completely elucidated but clearly involve regulation at the level of transcription. We previously identified a novel 19-base pair (bp) transcriptional regulatory element in the promoter region of the rat β4 subunit gene. This 19-bp element interacts specifically with DNA-binding proteins enriched in nuclear extracts prepared from adult rat brain. Using a combination of cellulose-phosphate, DNA-cellulose, and DNA sequence-specific affinity chromatographies, we purified the 19-bp element binding activity approximately 19,000-fold. Analysis by denaturing gel electrophoresis revealed the presence of four polypeptides in the most purified fraction, ranging in molecular masses between 31 and 114 kDa. Peptide sequence analysis revealed that one of the polypeptides is the bovine homologue of the transcriptional regulatory factor, Purα. Electrophoretic mobility shift assays indicated that Purα interacts directly and specifically with the 19-bp element. In addition, mobility shift assays using an anti-Purα monoclonal antibody revealed the presence of Purα, or an immunologically related protein, in nuclear extracts prepared from brain tissue. We hypothesize that the interaction between Purα and the 19-bp element is critical for proper expression of the β4 subunit gene.
MR regional perfusion imaging: visualizing functional collateral circulation.

SUMMARY We applied regional perfusion imaging (RPI), a new arterial spin-labeling MR imaging method that selectively studies regions of the brain perfused by individual carotid and basilar arteries. In a patient with cerebrovascular disease, RPI showed cerebral tissue perfused by pial collateral vessels, thereby demonstrating the relationship between anatomic and functional information, which was lacking in conventional x-ray angiography. RPI may be useful to study functional collateral circulation and hence guide therapy in ischemic disease.
In Vitro Activity of the New Oxazolidinone AZD2563 against Enterococci

ABSTRACT The activity of a new oxazolidinone antimicrobial, AZD2563, was assessed against >500 clinical isolates of enterococci representing six species. All isolates, including those resistant to other antibiotic classes, were inhibited by AZD2563 at concentrations ≤2 μg/ml, except for four strains resistant to linezolid. In most cases, AZD2563 was twofold more active than linezolid against enterococci.
Paradoxical Blood Flow Responses in the Diabetic Neuropathic Foot: an Assessment of the Contribution of Vascular Denervation and Microangiopathy

Blood flow is abnormal in the diabetic neuropathic foot, and this may be of importance in the pathogenesis of complications. Arteriovenous shunting is increased, and blood flow through these channels may paradoxically decrease in response to local heating. Peak skin blood flow is also reduced in these patients. It is not known whether these blood flow abnormalities may reflect diabetic microangiopathy, or whether they simply reflect vascular denervation. The skin blood flow response to a local thermal stimulus was studied in four non‐diabetic patients with a unilateral traumatic neuropathy and foot ulceration. All showed a decrease in skin blood flow (to 68% of basal) at the great toe during local heating in the neuropathic limb, in contrast to the normal limb, in which blood flow increased to 180% of basal. Peak skin blood flow was also greatly reduced in the neuropathic limb, being only 29% of the normal limb. Neuropathy alone can be responsible for abnormal skin blood flow responses in the neuropathic foot.
High Frequency of Histamine-Producing Bacteria in the Enological Environment and Instability of the Histidine Decarboxylase Production Phenotype

ABSTRACT Lactic acid bacteria contribute to wine transformation during malolactic fermentation. They generally improve the sensorial properties of wine, but some strains produce histamine, a toxic substance that causes health issues. Histamine-producing strains belong to species of the genera Oenococcus, Lactobacillus, and Pediococcus. All carry an hdcA gene coding for a histidine decarboxylase that converts histidine into histamine. For this study, a method based on quantitative PCR and targeting hdcA was developed to enumerate these bacteria in wine. This method was efficient for determining populations of 1 to 107 CFU per ml. An analysis of 264 samples collected from 116 wineries of the same region during malolactic fermentation revealed that these bacteria were present in almost all wines and at important levels, exceeding 103 CFU per ml in 70% of the samples. Histamine occurred at an often important level in wines containing populations of the above-mentioned bacteria. Fifty-four colonies of histamine producers isolated from four wines were characterized at the genetic level. All were strains of Oenococcus oeni that grouped into eight strain types by randomly amplified polymorphic DNA analysis. Some strains were isolated from wines collected in distant wineries. Moreover, hdcA was detected on a large and possibly unstable plasmid in these strains of O. oeni. Taken together, the results suggest that the risk of histamine production exists in almost all wines and is important when the population of histamine-producing bacteria exceeds 103 per ml. Strains of O. oeni producing histamine are frequent in wine during malolactic fermentation, but they may lose this capacity during subcultures in the laboratory.
The SL1-SL2 (Stem-Loop) Domain Is the Primary Determinant for Stability of the Gamma Retroviral Genomic RNA Dimer*

Retroviral genomes are assembled from two sense-strand RNAs by noncovalent interactions at their 5′ ends, forming a dimer. The RNA dimerization domain is a potential target for antiretroviral therapy and represents a compelling RNA folding problem. The fundamental dimerization unit for the Moloney murine sarcoma gamma retrovirus spans a 170-nucleotide minimal dimerization active sequence. In the dimer, two self-complementary sequences, PAL1 and PAL2, form intermolecular duplexes, and an SL1-SL2 (stem-loop) domain forms loop-loop base pairs, mediated by GACG tetraloops, and extensive tertiary interactions. To develop a framework for assembly of the retroviral RNA dimer, we quantified the stability of and established nucleotide resolution secondary structure models for sequence variants in which each motif was compromised. Base pairing and tertiary interactions between SL1-SL2 domains contribute a large free energy increment of -10 kcal/mol. In contrast, even though the PAL1 and PAL2 intermolecular duplexes span 10 and 16 bp in the dimer, respectively, they contribute only -2.5 kcal/mol to stability, roughly equal to a single new base pair. First, these results emphasize that the energetic costs for disrupting interactions in the monomer state nearly balance the PAL1 and PAL2 base pairing interactions that form in the dimer. Second, intermolecular duplex formation plays a biological role distinct from simply stabilizing the structure of the retroviral genomic RNA dimer.