Small LEA proteins as an effective air-water interface protectant for fragile samples during cryo-EM grid plunge freezing

Sample loss due to air-water interface (AWI) interactions is a significant challenge during cryo-electron microscopy (cryo-EM) sample grid plunge freezing. We report that small Late Embryogenesis Abundant (LEA) proteins, which naturally bind to AWI, can protect samples from AWI damage during plunge freezing. This protection is demonstrated with two LEA proteins from nematodes and tardigrades, which rescued the cryo-EM structural determination outcome of two fragile multisubunit protein complexes.

Models for human telomere C-strand fill-in by CST-Polα-primase

Telomere maintenance is essential for the genome integrity of eukaryotes, and this function is underpinned by the two-step telomeric DNA synthesis process: telomere G-overhang extension by telomerase and complementary strand fill-in by DNA polymerase alpha-primase (polα-primase). Compared to the telomerase step, the telomere C-strand fill-in mechanism is less understood. Recent studies have provided new insights into how telomeric single-stranded DNA-binding protein CTC1-STN1-TEN1 (CST) and polα-primase coordinate to synthesize the telomeric C-strand for telomere overhang fill-in. Cryogenic electron microscopy (cryo-EM) structures of CST-polα-primase complexes have provided additional insights into how they assemble at telomeric templates and de novo synthesize the telomere C-strand. In this review, we discuss how these latest findings coalesce with existing understanding to develop a human telomere C-strand fill-in mechanism model.

Structures of human primosome elongation complexes

The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers.

Structures of the human CST-Polα-primase complex bound to telomere templates

The mammalian DNA polymerase-α-primase (Polα-primase) complex is essential for DNA metabolism, providing the de novo RNA-DNA primer for several DNA replication pathways^1-4 such as lagging-strand synthesis and telomere C-strand fill-in. The physical mechanism underlying how Polα-primase, alone or in partnership with accessory proteins, performs its complicated multistep primer synthesis function is unknown. Here we show that CST, a single-stranded DNA-binding accessory protein complex for Polα-primase, physically organizes the enzyme for efficient primer synthesis. Cryogenic electron microscopy structures of the CST-Polα-primase preinitiation complex (PIC) bound to various types of telomere overhang reveal that template-bound CST partitions the DNA and RNA catalytic centres of Polα-primase into two separate domains and effectively arranges them in RNA-DNA synthesis order. The architecture of the PIC provides a single solution for the multiple structural requirements for the synthesis of RNA-DNA primers by Polα-primase. Several insights into the template-binding specificity of CST, template requirement for assembly of the CST-Polα-primase PIC and activation are also revealed in this study.

Lipid nanoparticle formulations for optimal RNA-based topical delivery to murine airways

INTRODUCTION

Lipid nanoparticles (LNP) have been successfully used as a platform technology for delivering nucleic acids to the liver. To broaden the application of LNPs in targeting non-hepatic tissues, we developed LNP-based RNA therapies (siRNA or mRNA) for the respiratory tract. Such optimized LNP systems could offer an early treatment strategy for viral respiratory tract infections such as COVID-19.

METHODS

We generated a small library of six LNP formulations with varying helper lipid compositions and characterized their hydrodynamic diameter, size distribution and cargo entrapment properties. Next, we screened these LNP formulations for particle uptake and evaluated their potential for transfecting mRNA encoding green fluorescence protein (GFP) or SARS-CoV2 nucleocapsid-GFP fusion reporter gene in a human airway epithelial cell line in vitro. Following LNP-siGFP delivery, GFP protein knockdown efficiency was assessed by flow cytometry to determine %GFP+ cells and median fluorescence intensity (MFI) for GFP. Finally, lead LNP candidates were validated in Friend leukemia virus B (FVB) male mice via intranasal delivery of an mRNA encoding luciferase, using in vivo bioluminescence imaging.

RESULTS

Dynamic light scattering revealed that all LNP formulations contained particles with an average diameter of <100 nm and a polydispersity index of <0.2. Human airway epithelial cell lines in culture internalized LNPs with differential GFP transfection efficiencies (73-97%). The lead formulation LNP6 entrapping GFP or Nuc-GFP mRNA demonstrated the highest transfection efficiency (97%). Administration of LNP-GFP siRNA resulted in a significant reduction of GFP protein expression. For in vivo studies, intranasal delivery of LNPs containing helper lipids (DSPC, DOPC, ESM or DOPS) with luciferase mRNA showed significant increase in luminescence expression in nasal cavity and lungs by at least 10 times above baseline control.

CONCLUSION

LNP formulations enable the delivery of RNA payloads into human airway epithelial cells, and in the murine respiratory system; they can be delivered to nasal mucosa and lower respiratory tract via intranasal delivery. The composition of helper lipids in LNPs crucially modulates transfection efficiencies in airway epithelia, highlighting their importance in effective delivery of therapeutic products for airways diseases.

Gender, ethnic difference in arrhythmic risks and prognosis in patients with non-ischaemic cardiomyopathy

Funding Acknowledgements

Type of funding sources: None.

Background

The mortality benefits of Automatic Intracardiac Defibrillator (AICD) in non-ischaemic cardiomyopathy patients is less clear. Subgroup analysis of Definite trial showed that female patients favoured medical treatment. Ethnic difference in arrhythmic risk also not known.

Method

447 patients with heart failure and reduced left ventricular ejection fraction (LVEF &lt;40%) due to non-ischemic cardiomyopathy, all have coronary angiogram to exclude significant coronary artery disease (&gt;70% stenosis).

Continuous variables were compared by Student t tests and categorical variables compared by use of the Fisher exact test. Composite endpoints include death, sudden cardiac death (SCD), ventricular arrhythmias (VA ) and hospitalisations for heart failure. P&lt;0.05 was denoted as statistical significant.

Results

Mean age 63.07 ± 14.19 years, male patients 314 (70%), 360 Chinese and 87 non-chinese. Mean age of male and female patients were 61.21 ± 13.65 and 67.46 ± 14.52 years old respectively. Patients with diabetes mellitus 38%, hypertension 76%, atrial fibrillation 38%, stroke 9%. LDL 2.78 ± 1.04 mmol/l, HbA1c 6.56 ± 1.62%, baseline creatinine 98.43 ± 37.27umol/l. Patients taking ivabradine 9%, b-blocker 88%, Angiotensin inhibitors/Angiotensin Receptor Blocker 66%, Sacubitrial/ Valsartan 26%, spironolactone 57%, SGLT-2 inhibitor 9%.

Mean follow-up duration of 6.18 ± 4.16 years. There were 61 deaths (13%, 2.20% death/ year, 20 females and 41 males). 38 SCD, 22 VA, 218 hospitalisation for heart failure

There was a significant increase in LVEF from 24.88 ± 8.17 to 39.92 ± 13.88% and 22.05 ± 8.52 to 36.14 ± 8.17 % in female and male patients respectively (p=0.023). 190 patients (43%) have LVEF increased to or more than 35%.

40 patients (9%) received device therapy (AICD and Cardiac resynchronization therapy), 19% secondary prevention, 81% for primary prevention. The median time from diagnosis of NICMP to appropriate device therapy for VT/ VT storms was 85.5 months (interquartile range 35-131). 18/21 patients (86%) noted to have appropriate therapy for VT/ VT storms were males. HR for males 8, 95% CI (1.06, 60.34, p=0.044). All the device therapy occurred in patients with LVEF&lt; 35%. There is also gender difference in composite endpoints (p=0.0022)

LVEF improved from 23.31± 8.67 to 38.10 ±15.20 and 21.63 ±7.57 to 33.74 ±12.92% respectively (p=0.014) in Chinese and non-Chinese patients respectively. There are no significant difference in the VA or primary composite endpoints.

Conclusions

The study showed progressive improvement of the therapeutic regimens improve mortality by improving LVEF regardless of gender or ethnicity. The ventricular tachyarrhythmic risk, composite endpoints are significantly higher in male than female patients with non-ischaemic cardiomyopathy. There is no ethnic difference in clinical endpoints.

CST does not evict elongating telomerase but prevents initiation by ssDNA binding

The CST complex (CTC1-STN1-TEN1) has been shown to inhibit telomerase extension of the G-strand of telomeres and facilitate the switch to C-strand synthesis by DNA polymerase alpha-primase (pol α-primase). Recently the structure of human CST was solved by cryo-EM, allowing the design of mutant proteins defective in telomeric ssDNA binding and prompting the reexamination of CST inhibition of telomerase. The previous proposal that human CST inhibits telomerase by sequestration of the DNA primer was tested with a series of DNA-binding mutants of CST and modeled by a competitive binding simulation. The DNA-binding mutants had substantially reduced ability to inhibit telomerase, as predicted from their reduced affinity for telomeric DNA. These results provide strong support for the previous primer sequestration model. We then tested whether addition of CST to an ongoing processive telomerase reaction would terminate DNA extension. Pulse-chase telomerase reactions with addition of either wild-type CST or DNA-binding mutants showed that CST has no detectable ability to terminate ongoing telomerase extension in vitro. The same lack of inhibition was observed with or without pol α-primase bound to CST. These results suggest how the switch from telomerase extension to C-strand synthesis may occur.

Shaping human telomeres: from shelterin and CST complexes to telomeric chromatin organization

The regulation of telomere length in mammals is crucial for chromosome end-capping and thus for maintaining genome stability and cellular lifespan. This process requires coordination between telomeric protein complexes and the ribonucleoprotein telomerase, which extends the telomeric DNA. Telomeric proteins modulate telomere architecture, recruit telomerase to accessible telomeres and orchestrate the conversion of the newly synthesized telomeric single-stranded DNA tail into double-stranded DNA. Dysfunctional telomere maintenance leads to telomere shortening, which causes human diseases including bone marrow failure, premature ageing and cancer. Recent studies provide new insights into telomerase-related interactions (the 'telomere replisome') and reveal new challenges for future telomere structural biology endeavours owing to the dynamic nature of telomere architecture and the great number of structures that telomeres form. In this Review, we discuss recently determined structures of the shelterin and CTC1-STN1-TEN1 (CST) complexes, how they may participate in the regulation of telomere replication and chromosome end-capping, and how disease-causing mutations in their encoding genes may affect specific functions. Major outstanding questions in the field include how all of the telomere components assemble relative to each other and how the switching between different telomere structures is achieved.

The structure of human CST reveals a decameric assembly bound to telomeric DNA

The CTC1-STN1-TEN1 (CST) complex is essential for telomere maintenance and resolution of stalled replication forks genome-wide. Here, we report the 3.0-angstrom cryo-electron microscopy structure of human CST bound to telomeric single-stranded DNA (ssDNA), which assembles as a decameric supercomplex. The atomic model of the 134-kilodalton CTC1 subunit, built almost entirely de novo, reveals the overall architecture of CST and the DNA-binding anchor site. The carboxyl-terminal domain of STN1 interacts with CTC1 at two separate docking sites, allowing allosteric mediation of CST decamer assembly. Furthermore, ssDNA appears to staple two monomers to nucleate decamer assembly. CTC1 has stronger structural similarity to Replication Protein A than the expected similarity to yeast Cdc13. The decameric structure suggests that CST can organize ssDNA analogously to the nucleosome's organization of double-stranded DNA.

Tailoring the homing capacity of human Tregs for directed migration to sites of Th1-inflammation or intestinal regions

Cell-based therapy with CD4⁺ FOXP3⁺ regulatory T cells (Tregs) is a promising strategy to limit organ rejection and graft-vs-host disease. Ongoing clinical applications have yet to consider how human Tregs could be modified to direct their migration to specific inflammation sites and/or tissues for more targeted immunosuppression. We show here that stable, homing-receptor-tailored human Tregs can be generated from thymic Tregs isolated from pediatric thymus or adult blood. To direct migration to Th1-inflammatory sites, addition of interferon-γ and IL-12 during Treg expansion produced suppressive, epigenetically stable CXCR3⁺ TBET⁺ FOXP3⁺ T helper (Th)1-Tregs. CXCR3 remained expressed after injection in vivo and Th1-Tregs migrated efficiently towards CXCL10 in vitro. To induce tissue-specific migration, addition of retinoic acid (RA) during Treg expansion induced expression of the gut-homing receptors α4β7-integrin and CCR9. FOXP3⁺ RA-Tregs had elevated expression of the functional markers latency-associated peptide and glycoprotein A repetitions predominant, increased suppressive capacity in vitro and migrated efficiently to healthy and inflamed intestine after injection into mice. Homing-receptor-tailored Tregs were epigenetically stable even after long-term exposure to inflammatory conditions, suppressive in vivo and characterized by Th1- or gut-homing-specific transcriptomes. Tailoring human thymic Treg homing during in vitro expansion offers a new and clinically applicable approach to improving the potency and specificity of Treg therapy.

Reconstitution of human shelterin complexes reveals unexpected stoichiometry and dual pathways to enhance telomerase processivity

The human shelterin proteins associate with telomeric DNA to confer telomere protection and length regulation. They are thought to form higher-order protein complexes for their functions, but studies of shelterin proteins have been mostly limited to pairs of proteins. Here we co-express various human shelterin proteins and find that they form defined multi-subunit complexes. A complex harboring both TRF2 and POT1 has the strongest binding affinity to telomeric DNA substrates comprised of double-stranded DNA with a 3′ single-stranded extension. TRF2 interacts with TIN2 with an unexpected 2:1 stoichiometry in the context of shelterin (RAP1₂:TRF2₂:TIN2₁:TPP1₁:POT1₁). Tethering of TPP1 to the telomere either via TRF2–TIN2 or via POT1 gives equivalent enhancement of telomerase processivity. We also identify a peptide region from TPP1 that is both critical and sufficient for TIN2 interaction. Our findings reveal new information about the architecture of human shelterin and how it performs its functions at telomeres.

The human shelterin complex protects telomere ends from being recognized as damaged DNA sites and regulates telomere length in conjunction with telomerase. Here the authors establish the stoichiometries of human shelterin complexes of various compositions and show shelterin provides dual pathways to stimulate telomerase processivity.

A magnetically actuated cellular strain assessment tool for quantitative analysis of strain induced cellular reorientation and actin alignment

Commercially available cell strain tools, such as pneumatically actuated elastomer substrates, require special culture plates, pumps, and incubator setups. In this work, we present a magnetically actuated cellular strain assessment tool (MACSAT) that can be implemented using off-the-shelf components and conventional incubators. We determine the strain field on the MACSAT elastomer substrate using numerical models and experimental measurements and show that a specific region of the elastomer substrate undergoes a quasi-uniaxial 2D stretch, and that cells confined to this region of the MACSAT elastomer substrate undergo tensile, compressive, or zero axial strain depending on their angle of orientation. Using the MACSAT to apply cyclic strain on endothelial cells, we demonstrate that actin filaments within the cells reorient away from the stretching direction, towards the directions of minimum axial strain. We show that the final actin orientation angles in strained cells are spread over a region of compressive axial strain, confirming previous findings on the existence of a varied pre-tension in the actin filaments of the cytoskeleton. We also demonstrate that strained cells exhibit distinctly different values of actin alignment coherency compared to unstrained cells and therefore propose that this parameter, i.e., the coherency of actin alignment, can be used as a new readout to determine the occurrence/extent of actin alignment in cell strain experiments. The tools and methods demonstrated in this study are simple and accessible and can be easily replicated by other researchers to study the strain response of other adherent cells.

α-Integrin expression and function modulates presentation of cell surface calreticulin

Calreticulin presentation on the cell surface is an important hallmark of immunogenic cell death (ICD), serving as the prophagocytic signal for macrophages. Cell adhesion is a physiologically relevant stimulus previously shown to increase calreticulin interaction with α-integrins via the juxtamembrane, cytosolic GFFKR motif. This study assessed whether integrin function can regulate surface calreticulin levels in ICD. We generated calreticulin-null T-lymphoblasts and confirmed the loss of surface calreticulin expression on cells treated with doxorubicin, an ICD inducer. Reconstituted expression with full-length calreticulin targeted to the endoplasmic reticulum (ER) successfully rescued doxorubicin-induced surface calreticulin. Reconstitution with a truncation mutant calreticulin targeted to the cytosol led to constitutively high surface calreticulin that was not further elevated by doxorubicin, suggesting calreticulin released from the stressed ER transits the cytosol before its translocation to the cell surface. When stimulated to engage integrin substrates, doxorubicin-treated wild-type T-lymphoblasts exhibited decreased surface calreticulin compared with cells under non-adherent conditions. The inhibitory effect on surface calreticulin was recapitulated for cells in suspension treated with a β1-integrin-activating antibody, 9EG7. Similarly, cells expressing a truncated α-integrin cytosolic tail, bearing only the juxtamembrane GFFKR calreticulin-binding motif, exhibited low surface calreticulin with doxorubicin treatment under non-adherent conditions. Using partial permeabilization techniques to distinguish between cytosolic and ER staining, we found that ICD inducers promoted the accumulation of cytosolic calreticulin with negligible change in total calreticulin, suggesting that integrin-mediated inhibition of surface calreticulin was due to reduced cytosolic to surface translocation. T-lymphoblasts co-treated with an ICD inducer and 9EG7 exhibited reduced phagocytosis by macrophages when compared with treatment with only ICD inducer. This study reveals a previously uncharacterized function of integrins as negative regulators of ICD by suppressing presentation of cell surface calreticulin.

Complex kinetics of DNA condensation revealed through DNA twist tracing

Toroid formation is an important mechanism for DNA condensation in cells. The length change during DNA condensation was investigated in previous single-molecule experiments. However, DNA twist is key to understanding the topological kinetics of DNA condensation. In this study, DNA twist as well as DNA length was traced during the DNA condensation by the freely orbiting magnetic tweezers and the tilted magnetic tweezers combined with Brownian dynamics simulations. The experimental results disclose the complex relationship between DNA extension and backbone rotation. Brownian dynamics simulations show that the toroid formation follows a wiggling pathway which leads to the complex DNA backbone rotation as revealed in our experiments. These findings provide the complete description of multivalent cation-dependent DNA toroid formation under tension.

Using pictograms to assist caregivers in liquid medication administration: a systematic review

WHAT IS KNOWN AND OBJECTIVE

It has been reported that more than 80% of out-of-hospital medication errors among the young children involve liquid formulations. The usefulness of pictorial aids to improve communication of medication instructions has not been extensively investigated for child health. The objective of this study was to determine the effectiveness of pictorial aids used to assist caregivers in the administration of liquid medications.

METHODS

MEDLINE, CINAHL, PsycINFO, ScienceDirect, Scopus and the Cochrane Library were searched for articles published up to February 2015. Studies that used pictorial aids with liquid medications and measured at least one of the following outcomes were included: dosing accuracy, comprehension of medication instructions, recall of information and adherence of caregivers. Two authors independently selected studies, extracted data and assessed methodological quality of studies using the Cochrane Collaboration's tool.

RESULTS AND DISCUSSION

Five experimental studies (four hospital based and one community based) with a total of 962 participants were included. A wide range of liquid formulations were studied, including both prescription and over-the-counter medications. The existing findings suggest that pictographic interventions reduced dosing errors, enhanced comprehension and recall of medication instructions and improved adherence of caregivers. Incorporating pictorial aids into verbal medication counselling or text-based instructions was more beneficial than using the single approach alone. Mixed results were identified for the relationship between health literacy of caregivers and effectiveness of pictorial aids.

WHAT IS NEW AND CONCLUSION

The evidence remains limited due to the small number of studies found and variations in methodological quality. This review suggests that pictorial aids might be potential interventions, but more high-quality studies are needed to support the routine use of any pictogram-based materials with liquid medications in the clinical settings.

The orally active urotensin receptor antagonist, KR36676, attenuates cellular and cardiac hypertrophy

BACKGROUND AND PURPOSE

Blockade of the actions of urotensin-II (U-II) mediated by the urotensin (UT) receptor should improve cardiac function and prevent cardiac remodelling in cardiovascular disease. Here, we have evaluated the pharmacological properties of the recently identified UT receptor antagonist, 2-(6,7-dichloro-3-oxo-2H-benzo[b][1,4]oxazin-4(3H)-yl)-N-methyl-N-(2-(pyrrolidin-1-yl)-1-(4-(thiophen-3-yl)phenyl) ethyl)acetamide (KR36676).

EXPERIMENTAL APPROACH

Pharmacological properties of KR36676 were studied in a range of in vitro assays (receptor binding, calcium mobilization, stress fibre formation, cellular hypertrophy) and in vivo animal models such as cardiac hypertrophy induced by transverse aortic constriction (TAC) or myocardial infarction (MI).

KEY RESULTS

KR36676 displayed high binding affinity for the UT receptor (Ki : 0.7 nM), similar to that of U-II (0.4 nM), and was a potent antagonist at that receptor (IC50 : 4.0 nM). U-II-induced stress fibre formation and cellular hypertrophy were significantly inhibited with low concentrations of KR36676 (≥0.01 μM). Oral administration of KR36676 (30 mg·kg(-1) ) in a TAC model in mice attenuated cardiac hypertrophy and myocardial fibrosis. Moreover, KR36676 restored cardiac function and myocyte size in rats with MI-induced cardiac hypertrophy.

CONCLUSIONS AND IMPLICATIONS

A highly potent UT receptor antagonist exerted anti-hypertrophic effects not only in infarcted rat hearts but also in pressure-overloaded mouse hearts. KR36676 could be a valuable pharmacological tool in elucidating the complicated physiological role of U-II and UT receptors in cardiac hypertrophy.

Dynamics and stability of polymorphic human telomeric G-quadruplex under tension

As critical DNA structures capping the human chromosome ends, the stability and structural polymorphism of human telomeric G-quadruplex (G4) have drawn increasing attention in recent years. This work characterizes the equilibrium transitions of single-molecule telomeric G4 at physiological K⁺ concentration. We report three folded states of telomeric G4 with markedly different lifetime and mechanical stability. Our results show that the kinetically favored folding pathway is through a short-lived intermediate state to a longer-lived state. By examining the force dependence of transition rates, the force-dependent transition free energy landscape for this pathway is determined. In addition, an ultra-long-lived form of telomeric G4 structure with a much stronger mechanical stability is identified.

Single-molecule studies on the mechanical interplay between DNA supercoiling and H-NS DNA architectural properties

The Escherichia coli H-NS protein is a major nucleoid-associated protein that is involved in chromosomal DNA packaging and gene regulatory functions. These biological processes are intimately related to the DNA supercoiling state and thus suggest a direct relationship between H-NS binding and DNA supercoiling. Here, we show that H-NS, which has two distinct DNA-binding modes, is able to differentially regulate DNA supercoiling. H-NS DNA-stiffening mode caused by nucleoprotein filament formation is able to suppress DNA plectoneme formation during DNA supercoiling. In contrast, when H-NS is in its DNA-bridging mode, it is able to promote DNA plectoneme formation during DNA supercoiling. In addition, the DNA-bridging mode is able to block twists diffusion thus trapping DNA in supercoiled domains. Overall, this work reveals the mechanical interplay between H-NS and DNA supercoiling which provides insights to H-NS organization of chromosomal DNA based on its two distinct DNA architectural properties.

Mechanism of DNA organization by Mycobacterium tuberculosis protein Lsr2

Bacterial nucleoid-associated proteins, such as H-NS-like proteins in Enterobacteriaceae, are abundant DNA-binding proteins that function in chromosomal DNA organization and gene transcription regulation. The Mycobacterium tuberculosis Lsr2 protein has been proposed to be the first identified H-NS analogue in Gram-positive bacteria based on its capability to complement numerous in vivo functions of H-NS. Here, we report that Lsr2 cooperatively binds to DNA forming a rigid Lsr2 nucleoprotein complex that restricts DNA accessibility, similar to H-NS. On large DNA, the rigid Lsr2 nucleoprotein complexes can mediate DNA condensation into highly compact DNA conformations. In addition, the responses of Lsr2 nucleoprotein complex to environmental factors (salt concentration, temperature and pH) were studied over physiological ranges. These results provide mechanistic insights into how Lsr2 may mediate its gene silencing, genomic DNA protection and organization functions in vivo. Finally, our results strongly support that Lsr2 is an H-NS-like protein in Gram-positive bacteria from a structural perspective.

Oxidative torrefaction of biomass residues and densification of torrefied sawdust to pellets

Oxidative torrefaction of sawdust with a carrier gas containing 3-6% O(2) was investigated in a TG and a fluidized bed reactor, with the properties of the torrefied sawdust and pellets compared with traditional torrefaction without any O(2), as well as the dry raw material. It is found that the oxidative torrefaction process produced torrefied sawdust and pellets of similar properties as normally torrefied sawdust and corresponding pellets, especially on the density, energy consumption for pelletization, higher heating value and energy yield. For moisture absorption and hardness of the torrefied pellets, the oxidative torrefaction process showed slightly poor but negligible performance. Therefore, it is feasible to use oxygen laden combustion flue gases as the carrier gas for torrefaction of biomass. Besides, torrefied sawdust can be made into dense and strong pellets of high hydrophobicity at a higher die temperature than normally used in the production of traditional control pellets.

The nucleoid-associated protein Dan organizes chromosomal DNA through rigid nucleoprotein filament formation in E. coli during anoxia

Dan is a transcription factor that regulates the ttd operon encoding tartrate dehydratase. During anaerobic conditions, its copy number increases by 100-fold, making Dan an abundant nucleoid-associated protein. However, little is known about the mode of Dan–DNA interaction. To understand its cellular functions, we used single-molecule manipulation and imaging techniques to show that Dan binds cooperatively along DNA, resulting in formation of a rigid periodic nucleoprotein filament that strongly restricts accessibility to DNA. Furthermore, in the presence of physiologic levels of magnesium, these filaments interact with each other to cause global DNA condensation. Overall, these results shed light on the architectural role of Dan in the compaction of Escherichia coli chromosomal DNA under anaerobic conditions. Formation of the nucleoprotein filament provides a basis in understanding how Dan may play roles in both chromosomal DNA protection and gene regulation.

Nucleoprotein filament formation is the structural basis for bacterial protein H-NS gene silencing

H-NS is an abundant nucleoid-associated protein in bacteria that globally silences genes, including horizontally-acquired genes related to pathogenesis. Although it has been shown that H-NS has multiple modes of DNA-binding, which mode is employed in gene silencing is still unclear. Here, we report that in H-NS mutants that are unable to silence genes, are unable to form a rigid H-NS nucleoprotein filament. These results indicate that the H-NS nucleoprotein filament is crucial for its gene silencing function, and serves as the fundamental structural basis for gene silencing by H-NS and likely other H-NS-like bacterial proteins.

Torrefaction of sawdust in a fluidized bed reactor

In the present work, stable fluidization of sawdust was achieved in a bench fluidized bed with an inclined orifice distributor without inert bed materials. A solids circulation pattern was established in the bed without the presence of slugging and channeling. The effects of treatment severity and weight loss on the solid product properties were identified. The decomposition of hemicelluloses was found to be responsible for the significant changes of chemical, physical and mechanical properties of the torrefied sawdust, including energy content, particle size distribution and moisture absorption capacity. The hydrophobicity of the torrefied sawdust was improved over the raw sawdust with a reduction of around 40 wt.% in saturated water uptake rate, and enhanced with increasing the treatment severity due to the decomposition of hemicelluloses which are rich in hydroxyl groups. The results in this study provided the basis for torrefaction in fluidized bed reactors.

Gene silencing H-NS paralogue StpA forms a rigid protein filament along DNA that blocks DNA accessibility

Nucleoid-associated proteins are bacterial proteins that are responsible for chromosomal DNA compaction and global gene regulation. One such protein is Escherichia coli Histone-like nucleoid structuring protein (H-NS) which functions as a global gene silencer. Whereas the DNA-binding mechanism of H-NS is well-characterized, its paralogue, StpA which is also able to silence genes is less understood. Here we show that StpA is similar to H-NS in that it is able to form a rigid filament along DNA. In contrast to H-NS, the StpA filament interacts with a naked DNA segment to cause DNA bridging which results in simultaneous stiffening and bridging of DNA. DNA accessibility is effectively blocked after the formation of StpA filament on DNA, suggesting rigid filament formation is the important step in promoting gene silencing. We also show that >1 mM magnesium promotes higher order DNA condensation, suggesting StpA may also play a role in chromosomal DNA packaging.

WW domain-mediated interaction with Wbp2 is important for the oncogenic property of TAZ

The transcriptional co-activators YAP and TAZ are downstream targets inhibited by the Hippo tumor suppressor pathway. YAP and TAZ both possess WW domains, which are important protein–protein interaction modules that mediate interaction with proline-rich motifs, most commonly PPXY. The WW domains of YAP have complex regulatory roles as exemplified by recent reports showing that they can positively or negatively influence YAP activity in a cell and context-specific manner. In this study, we show that the WW domain of TAZ is important for it to transform both MCF10A and NIH3T3 cells and to activate transcription of ITGB2 but not CTGF, as introducing point mutations into the WW domain of TAZ (WWm) abolished its transforming and transcription-promoting ability. Using a proteomic approach, we discovered potential regulatory proteins that interact with TAZ WW domain and identified Wbp2. The interaction of Wbp2 with TAZ is dependent on the WW domain of TAZ and the PPXY-containing C-terminal region of Wbp2. Knockdown of endogenous Wbp2 suppresses, whereas overexpression of Wbp2 enhances, TAZ-driven transformation. Forced interaction of WWm with Wbp2 by direct C-terminal fusion of full-length Wbp2 or its TAZ-interacting C-terminal domain restored the transforming and transcription-promoting ability of TAZ. These results suggest that the WW domain-mediated interaction with Wbp2 promotes the transforming ability of TAZ.

Simple and inexpensive method of wood pellets macro-porosity measurement

A novel simplified stereometric measurement method for determining the macro-porosity of wood pellets through geometrical approach was successfully developed and tested. The irregular ends of pellets of circular cross-section were sanded flat so that their geometry becomes cylinder and their volumes evaluated using mensuration formula. Such formed cylindrical pellets were loose or tap filled to selected volumes to evaluate the macro-porosity and the constant specific weight. The method was extended to evaluate actual wood pellets properties. Overall macro-porosity of actual wood pellets was determined as 41.0+/-2.5% and 35.5+/-2.7%, mean bulk density as 670+/-29 kg m(-3) and 731+/-31 kg m(-3), and classified as "Class-3:Medium" and "Class-3&4:Medium to Low" for loose and tapped fills, respectively. Hausner ratio and Carr's compressibility index classify wood pellets as "freely flowing." The developed stereometric method can be used as a handy inexpensive laboratory procedure to estimate the macro-porosity of different types and makes of wood pellets and other similar packaged materials.

Permeability of wood pellets in the presence of fines

Broken pellets and fines are produced when pellets are handled. The resistance to air flow was measured for clean pellets and for pellets mixed with 1-20% broken pellets (fines). A pellet diameter was 6mm. The lengths ranged from 6 to 12 mm. Clean pellets were defined as particles that remained on a 4mm screen. A typical sieve analysis showed 30% of the mass of particles that passed through the 4mm screen was smaller than 1mm. The airflow rates used in the experiment ranged from 0.004 to 0.357 ms(-1). The corresponding pressure drop ranged from 1.9 to 271 Pam(-1) for clean pellets, from 4.8 to 1100 Pam(-1) for 10% fines content, and from 7.9 to 1800 Pam(-1) for 20% fines content. Coefficients of Hukill and Ives' equation were estimated for clean pellets and a multiplier was defined to calculate pressure drop for pellets mixed with fines.

Assessment of Physical Activity Level among Individuals with Type 2 Diabetes Mellitus at Cheras Health Clinic, Kuala Lumpur

A cross-sectional study was carried out to assess the physical activity levels among patients with type 2 diabetes mellitus (DM) at Cheras Health Clinic in Kuala Lumpur. A total of 132 subjects (62 men and 70 women) aged 30 years and above participated in this study. Data was collected using an interview based questionnaire to obtain socio-demographic and health profile information. Physical activity was assessed using a shortened version of the International Physical Activity Questionnaire (IPAQ). Anthropometric measurements and body fat were also taken. Glycaemic status, that is, HbA1c, fasting blood sugar (FBS) and 2 hours post-prandial (2-HPP) were obtained from medical records. Results showed that the mean age of the patients was 51.9 + 5.8 years. The majority of patients had poor glycaemic control based on HbA1c (70.7%), FBS (71.9%) and 2HPP (85.4%). Patients who were unmarried and aged(60 years and above had a lower physical activity level (p< 0.05). In the older age group, low physical activity was associated with poor glycaemic control (p< 0.05). Patients in the moderate and high physical activity level were motivated to perform physical activity so as to be healthy (68.1%). Low physical activity level among patients was due to lack of time (54.5%) and lack of energy (21.2%). In conclusion, physical activity levels of the patients were unsatisfactory and associated with poor glycaemic control, especially in the elderly. There is a need to encourage diabetic patients to undertake regular physical activity in order to achieve optimal glycaemic control.

Isolation and characterization of a phenol-degrading bacterium from an industrial activated sludge

This paper reports the successful isolation and characterization of a new phenol-degrading bacterium, strain EDP3, from activated sludge. Strain EDP3 is a nonmotile, strictly aerobic, Gram-negative, and short-rod or coccobacillary bacterium, which occurs singly, in pairs, or in clusters. 16S rRNA gene sequence analysis revealed that strain EDP3 belonged to the gamma group of Proteobacteria, with a 97.0% identity to 16S rRNA gene sequences of Acinetobacter calcoaceticus. Strain EDP3 could aerobically grow on a number of aromatic compounds, such as phenol, sodium benzoate, p-hydroxybenzoate, phenylacetate, benzene, ethylbenzene, benzylalcohol, and so on. In particular, it could mineralize up to 1,000 mg l(-1) phenol at room temperature (25 degrees C). The growth kinetics of strain EDP3 on phenol as a sole carbon and energy source at 25 degrees C can be described using the Haldane equation. It has a maximal specific growth rate (mu(max)) of 0.28 h(-1), a half-saturation constant (K(S)) of 1,167.1 mg l(-1), and a substrate inhibition constant (Ki) of 58.5 mg l(-1). Values of yield coefficient (Y(X/S)) are between 0.4 and 0.6 mg dry cell (mg phenol)(-1). Strain EDP3 has high tolerance to the toxicity of phenol (up to 1,000 mg l(-1)). It therefore could be an excellent candidate for the biotreatment of high-strength phenol-containing industrial wastewaters and for the in situ bioremediation of phenol-contaminated soils.

Enhancement of the sulfur capture capacity of limestones by the addition of Na2CO3 and NaCl

The ability of Na2CO3 and NaCl to enhance the sulfur capture capacity of three limestones was evaluated via fixed-bed calcination and sulfation experiments. The tested limestones represent three different sulfation morphologies: unreacted-core, network, and uniformly sulfated. Treatment with aqueous or powdered Na2CO3 significantly increased the Ca-utilization for two stones which normally sulfate in an unreacted-core pattern (20% to 45%) and network pattern (33% to 49%). The increase was lower for the uniformly sulfated stone (44% to 48%). Na2CO3 treatment increased the number of macropores leading to uniform sulfation of all particles, nearly eliminating the normal strong dependence of utilization on limestone type and particle size. The effect of Na2CO3 is believed to be associated with formation of a eutectic melt which enhances ionic diffusion and accelerates molecular rearrangement of the CaO. Treatment with aqueous NaCl solution caused a decrease in utilization, probably due to formation of large grains and plugging of pores caused by formation of a large amount of eutectic melt. The effect of Na2CO3 is less sensitive than that of NaCl to the amount added and the combustion environment (temperature and gas composition). In addition, Na2CO3 neither promotes corrosion nor forms chlorinated byproducts, which are main concerns associated with NaCl. Thus, Na2CO3 appears to have significant advantages over NaCl for enhancement of limestone sulfur capture capacity in fluidized-bed combustors.

Characterization and regulation of glutathione S-transferase gene from Schizosaccharomyces pombe

A glutathione S-transferase (GST) gene has been cloned from Schizosaccharomyces pombe for the first time. The nucleotide sequence determined was found to contain 2030 base pairs including an open reading frame of 229 amino acids that would encode a protein of a molecular mass of 27017 Da. The cloned GST gene was expressed and was found to function in S. pombe, Saccharomyces cerevisiae, and Escherichia coli. The plasmid pGT207 encoding the S. pombe GST gene appeared to be able to accelerate the growth of a wild type S. pombe culture. In a culture of S. pombe containing plasmid pGT207, the growth was inhibited less by mercuric chloride than in a culture with vector alone. The 1088 bp region upstream from the GST gene as well as the region encoding the N-terminal 14 amino acids was transferred into the promoterless beta-galactosidase gene of plasmid YEp357R to yield the fusion plasmid pYSH2000. beta-Galactosidase synthesis was induced by cadmium chloride, mercuric chloride, hydrogen peroxide, and menadione. It was also induced by high temperature. These results suggest that the cloned S. pombe GST gene is involved in the oxidative stress response.

Computational fluid dynamics study of a protruded-hinge bileaflet mechanical heart valve

BACKGROUND AND AIM OF THE STUDY

Following clinical experience with the Medtronic Parallel bileaflet mechanical heart valve, considerable interest has been shown in investigating fluid mechanics inside the hinge socket. Most of these studies involved hinges that are recessed into the valve housing, such as the St. Jude Medical (SJM), CarboMedics, Sorin and On-X bileaflet mechanical heart valves. The aim of this study was to investigate the flow fields of a protruded hinge under steady flow conditions, with the occluder in its fully open position. Computational fluid dynamics (CFD) simulation using the Fluent 4.4.7 commercial solver was applied in this investigation. This protruded hinge mechanism for pivoting the occluder is an in-house design from the Cardiovascular Dynamics Laboratory, Nanyang Technological University.

METHODS

The Fluent 4.4.7 code was run on a Silicon Graphic Inc. computer (4-CPUx185 MHz) in the CFD simulation. A body-fitted coordinates (BFC) grid was generated to cover the entire valvular flow domain, including the interior of the hinge and leaflet. Clearance between the leaflet and pivot housing was 50-70 microm. In the vicinity of the protruded hinge, mesh cells were small compared with hinge dimensions. A power law distribution of grid points was applied to optimize the number of cells used to cluster the entire flow field. The overall computational flow domain of the valve channel, including the floating leaflet and immersed hinge, was approximately 170,000 cells in total. Inside the hinge socket, approximately 10,000 cells were generated. A comparative model with recessed hinge that resembled the SJM valve hinge design was modeled. Due to geometric difficulties, an unstructured grid scheme was applied. Great attention was focused within the hinge pocket, in particular to the clearance between the hinge pivot and leaflet. A total of 2 million cells was generated for the whole computational flow domain.

RESULTS

Under steady flow conditions, with the leaflet fixed in an open position, the protruded hinge design yielded a pair of small vortices that formed behind the stoppers. A low-magnitude velocity was observed inside the hinge clearance. Vortices developed behind the protruded stopper. Migrating flow was noted beneath the leaflet clearance as a result of pressure difference across the leaflet. For the recessed hinge design, reverse flow dominated the inside of the hinge socket, and developed into a pair of vortices at high Reynolds number.

CONCLUSION

The protruded hinge mechanism was designed to expose the overall hinge region to the mainstream flow for a positive washing effect. Flow in this protruded hinge design is, in general, found to be three-dimensional. Initial results under steady flow conditions showed low laminar and turbulent shear stress, while the hinge clearance was well washed.

Cloning, expression and regulation of Schizosaccharomyces pombe gene encoding thioltransferase

The genomic DNA encoding thioltransferase was isolated from Schizosaccharomyces pombe using the polymerase chain reaction. The amplified DNA fragment was confirmed by Southern hybridization, completely digested with HindIII and BamHI, and then ligated into the yeast-Escherichia coli shuttle vector pRS316, which resulted in plasmid pEH1. The insert of plasmid pEH1 was transferred into the multi-copy vector YEp357 to generate plasmid pYEH1. The determined nucleotide sequence harbors an open reading frame consisting of four exons and three introns, which encodes a polypeptide of 101 amino acids with a molecular mass of 11261 Da. Thioltransferase activity was increased 1.6-fold in Saccharomyces cerevisiae containing plasmid pYEH1, and 1.8- and 2.7-fold in S. pombe containing plasmid pEH1 and pYEH1, respectively. The upstream sequence and the region encoding the N-terminal six amino acids were fused into promoterless beta-galactosidase gene of the shuttle vector YEp357R to generate the fusion plasmid pYEHR1. Synthesis of beta-galactosidase from the fusion plasmid was found to be enhanced by zinc and NO-generating S-nitroso-N-acetylpenicillamine.

Mammary gland tumor in transgenic mice expressing targeted beta-casein/HPV16E6 fusion gene

The human papillomaviruses (HPV)-16 and HPV-18 referred to as high-risk HPVs are strongly associated with anogenital malignancies as well as benign epithelial cysts. It has been demonstrated that transgenic mice carrying HPV-16 E6-E7 under the control of the MMTV LTR developed malignant tumors including salivary gland carcinoma, lymphoma, skin histiocytomas and testicular tumors in a non-mammary gland specific manner. Another regulatory unit of rat beta-casein gene can confer the expression of fusion gene preferentially in the mammary glands of transgenic mice in a developmentally regulated manner. In order to generate mammary tumor formation in transgenic mice directing HPV16E6 gene alone into the mammary gland, this regulatory unit was fused to the E6 gene of HPV-16 type to constructing fusion gene. By screening 51 newborn founder transgenic mice, three mice carrying transgenes were identified. One line termed TG32 developed in a mammary gland tumor with large subcutaneous mass in the left rib region at 17 months of age. The levels of E6 transcript in the mass-tumor of TG32 line were lower than those in non-tumor mammary gland of identical TG32 and of TG250. In each tissue of TG32 line, high expression of E6 transcript was detected both in the mammary gland and brain. Histological analysis showed that cells from mammary gland tumor of the TG32 line had also hyperplasia appearance, with irregular or increased total number of mitotic rate. These observations suggest that developing phenotype and the level of E6 transcripts in the process of malignant transformation may have different mechanisms involving the capacity to bind and destabilize p53, although for confirmation it is necessary to investigate many more transgenic mice.

Growth-phase regulation of the Escherichia coli thioredoxin gene

The two promoters of Escherichia coli trxA gene were separately cloned into pKO100 as well as pJEL170. Galactokinase expression in cells containing the pKO100 derivatives was found to be negatively correlated with growth rate and was 6- to 20-fold higher in stationary cultures than in exponential cultures. The expression of trxA-galK was induced by amino acid starvation in a RelA(+) strain but not in an isogenic Rel(-) strain indicating that the control involves guanosine 3',5'-bispyrophosphate (ppGpp). RpoS, which appears to be essential for expression of most stationary phase expressed genes, is not required for trxA expression. Increased expression of relA, which increases ppGpp concentration, increases trxA expression.

Cloning, nucleotide sequence and expression of thioltransferase (glutaredoxin) cDNA from Schizosaccharomyces pombe

Thioltransferase (TTase), also known as glutaredoxin (Grx), is an enzyme that catalyzes the reduction of a variety of disulfide compounds, including protein disulfides, in the presence of reduced glutathione. TTase acts as a cofactor for various enzymes such as ribonucleotide reductase. We previously purified a TTase from Schizosaccharomyces pombe and its molecular size was determined. In the present study, a cDNA coding TTase was isolated from a cDNA library of Schizosaccharomyces pombe by colony hybridization, which was constructed in a plasmid vector pGAD GH, and its corresponding insert was confirmed by Southern hybridization. The nucleotide sequence of the 375 bp long cDNA clone reveals an open reading frame, which encodes a protein of 101 amino acids. The coding region of the original clone was transferred after the lac promoter of pUC13 vector for expression in E. coli, and simultaneously, a suitable Shine-Dalgarno (SD) sequence was added in front of the coding region by PCR. The two primers used for PCR also separately contained BamHI and HindIII restriction sites. The E. coli strain (A434) harboring the pUC13 derivative pKU10 showed a 17.3-fold increase in TTase activity compared to the strain with only the vector plasmid.

Thioltransferase from Arabidopsis thaliana seed: purification to homogeneity and characterization

Thioltransferase is a general GSH-disulfide reductase of importance for redox regulation. The protein thioltransferase has been purified to apparent homogeneity on SDS-PAGE from the Arabidopsis thaliana seed. The purification procedures included DEAE-cellulose ion exchange chromatography, Sephadex G-75 gel filtration, Q-Sepharose ion exchange chromatography, and DEAE-Sephadex A-25 ion exchange chromatography. The enzyme has a molecular mass of 22 kDa and a pI of 4.8, and it is heatstable. The protein had broad specificities for substrates ranging from low-molecular disulfides (S-sulfocysteine and cystine) to protein disulfides (trypsin and insulin). However, it could not reduce the disulfide linkages of ribonuclease A and bovine serum albumin. It could utilize non-disulfide substrates such as dehydroascorbic acid and alloxan. The protein can reduce the disulfide bond in 2-hydroxyethyl disulfide with an optimum pH of 8.5. Its activity was greatly activated by monothiol compounds such as reduced glutathione and L-cysteine.

Thioltransferase from Schizosaccharomyces pombe: purification to homogeneity and some properties

Two types of thioltransferase were identified in the cytosolic extract of Schizosaccharomyces pombe, a fission yeast. In the present study, the major one of them was purified to homogeneity using chromatography processes such as ion-exchange chromatography and gel filtration. Purification was monitored by the transhydrogenase activity of thioltransferase with 2-hydroxyethyl disulfide as a substrate. Its molecular weight was estimated to be about 14,000 on SDS-polyacrylamide gel electrophoresis. The purified enzyme catalyzes the reduction of various disulfide compounds such as S-sulfocysteine, L-cystine, and insulin. It was also found to contain the reducing activity on non-disulfide substrates such as dehydroascorbic acid and alloxan. Its activity was greatly activated by high concentrations of reduced glutathione. It was found to be very heat-stable as like other thioltransferases. It was characterized on other aspects such as kinetic parameters and optimal reaction conditions.

A second form of phenylalanine ammonia-lyase from leaf mustard

Phenylalanine ammonia-lyase (PAL, EC 4.3.1.5) catalyzes the elimination of ammonium ion from L-phenylalanine in a variety of plants and fungal species. PAL was previously purified and characterized from leaf mustard in our laboratory. In the present study, we purified a second phenylalanine ammonia-lyase (PAL II) from leaf mustard by a combination of ion exchange chromatography and gel filtration. PAL I and PAL II migrate at a different rate on native polyacrylamide gel electrophoresis. It consists of four subunits, each having the molecular mass of about 37,000 Da. Its isoelectric point and Km value for L-phenylalanine were found to be 5.4 and 3.8 x 10(-5)M, respectively. The purified enzyme has an optimum pH and temperature of 8 and 45 degree C, respectively. It is activated about 2-fold by caffeic acid (1 mM), whereas it is inhibited to 15% by Zn2+ (1 mM). However, the physiological role of PAL II remains unknown.

Purification and properties of phenylalanine ammonia-lyase from leaf mustard

Phenylalanine ammonia-lyase (PAL, EC 4.3.1.5), the first enzyme in phenylpropanoid biosynthesis, catalyzes the elimination of ammonium ion from L-phenylalanine. In the present study, PAL was purified through ammonium sulfate fractionation, DEAE-cellulose chromatography, Sephadex G-200 chromatography, and Q-Sepharose chromatography from the cytosolic fraction of leaf mustard (Brassica juncea var. integrifolia). It consists of 4 subunits, each having an estimated molecular weight of about 40,000 on SDS-polyacrylamide gel electrophoresis (SDS-PAGE). The optimal pH and temperature of the purified enzyme are 9.0 and 45 degrees C, respectively. Its activity is inhibited by Zn2+ ion, and it is strongly activated by caffeic acid. The purified PAL seems to have some characteristics different from those obtained with other PALs.

Purification and characterization of glutaredoxin from Cryptococcus neoformans

Glutaredoxin, also known as thioltransferase, was purified from Cryptococcus neoformans by procedures including DEAE-cellulose ion exchange chromatography, Q-Sepharose ion-exchange chromatography, and gel filtration on Sephadex G-50. Its purity was confirmed by SDS-polyacrylamide gel electrophoresis and its molecular weight was estimated to be 12,000 Da. The purified enzyme has a K(m) value of 1.03 mM with 2-hydroxyethyl disulfide as a substrate. The enzyme also utilizes L-sulfocysteine, L-cystine, and bovine serum albumin as substrates in the presence of reduced glutathione. The enzyme has K(m) values of 0.34-2.50 mM for these substrates. It was greatly activated by thiol compounds such as reduced glutathione, dithiothreitol, L-cysteine and beta-mercaptoethanol. It is partially inactivated at 60 degrees C or higher temperatures. It plays an important role in thiol-disulfide exchange in Cryptococcus neoformans.

Nucleotide sequence and revised map location of the arn gene from bacteriophage T4

Non-glucosylated (Glu-) T-even phage DNAs are restricted by Escherichia coli RgIA and RgIB endonucleases with different specificities. RgIB endonuclease activity is strongly inhibited by anti-restriction endonuclease (Arn) encoded by the bacteriophage T4 genome. The nucleotide sequence of the arn gene encoding Arn was determined. The product of the cloned arn gene was overexpressed by the T7 RNA polymerase/promoter system, and its molecular size is consistent with that predicted from the open reading frame of the arn gene. The arn gene is located between the asiA gene and motA gene in the region of 161,300-161,578 nucleotides.

Arachidonic acid, a principal product of Rac-activated phospholipase A2, stimulates c-fos serum response element via Rho-dependent mechanism

Previously, we have reported that phospholipase A2 (PLA2) is one of the major downstream targets by which Rac GTPase mediates the activation of c-fos serum response element (SRE) in response to agonists such as EGF [FEBS Lett. 407 (1997) 7-12]. Thus, the potential activity of arachidonic acid (AA), a principal product of Rac-activated PLA2, on c-fos SRE stimulation has been suggested. Here, we provide evidence about the biological activity of AA on c-fos SRE activation. Further, we observed that co-transfection with expression plasmid of either RhoN19, a dominant negative RhoA mutant, or botulinum C3 transferase which inhibits Rho via ADP ribosylation, selectively repressed AA- or Rac-induced SRE activation, suggesting that Rho activity is critical for the signaling cascade of 'Rac-PLA2-AA' to c-fos SRE. Thus, Rac signaling to the nucleus appears to be, at least partly, mediated by a Rho-linked pathway and this Rac-Rho signaling connection is mediated by AA. In accordance with the role of Rho as a potential mediator of AA signaling to the nucleus, AA induces a rapid translocation of RhoA.

Expression of the Escherichia coli thioredoxin gene is negatively regulated by cyclic AMP

Regulation of the Escherichia coli thioredoxin gene (trxA) was studied using trxA-lac translational fusion constructed in the vector pMC1403. Synthesis of beta-galactosidase from the trxA-lac fusion was found to be repressed in the presence of lactose. A switch of carbon source from glucose to lactose and an addition of cyclic AMP (cAMP) caused a decrease in beta-galactosidase synthesis from the trxA-lac fusion. The repression effect of exogenous cAMP was not observed in the crp mutant strain. The beta-galactosidase synthesis from the trxA-lac fusion lacking a plausible cAMP-CRP binding site was not lowered in the presence of lactose or in the addition of cAMP. Expression of the chromosomal trxA gene was reduced by exogenous cAMP. These findings indicate that the expression of the trxA gene is controlled by cAMP in a negative manner.

Efficient detection of DNA polymorphisms by fluorescent RAPD analysis

A method is presented for the analysis of fluorescently labeled random amplified polymorphic DNA (FRAPD) fragments. A DNA sequencer and collection and analysis software were used to estimate the sizes of DNA fragments based on their mobilities relative to in-lane size markers. This allowed confident identification and comparison of FRAPD markers both within and between polyacrylamide gels. In comparison with analysis of RAPD products using ethidium bromide-stained agarose gels, fluorescent analysis improved the sensitivity, resolution and precision of sizing of RAPD products of about 50-2100 bp. FRAPD fragments produced from amplification of zebrafish DNA are informative as genetic markers that segregate with Mendelian inheritance. FRAPD analysis was found to be very efficient for identifying new DNA polymorphisms.

Identification of a third thioredoxin gene from Corynebacterium nephridii

We identified and sequenced a gene encoding a third thioredoxin (C3) from Corynebacterium nephridii. The determined nucleotide sequence encodes a thioredoxin of 145 amino acid residues, which is larger than most thioredoxins found in microbial cells and contains 6 cysteine residues. C. nephridii thioredoxin C3 is able to serve as a subunit of T7 DNA polymerase. C. nephridii is the first nonphotosynthetic procaryotic organism known to carry three different thioredoxins.