“Biofilmology”: a multidisciplinary review of the study of microbial biofilms

The observation of biofilm formation is not a new phenomenon. The prevalence and significance of biofilm and aggregate formation in various processes have encouraged extensive research in this field for more than 40 years. In this review, we highlight techniques from different disciplines that have been used to successfully describe the extracellular, surface and intracellular elements that are predominant in understanding biofilm formation. To reduce the complexities involved in studying biofilms, researchers in the past have generally taken a parts-based, disciplinary specific approach to understand the different components of biofilms in isolation from one another. Recently, a few studies have looked into combining the different techniques to achieve a more holistic understanding of biofilms, yet this approach is still in its infancy. In order to attain a global understanding of the processes involved in the formation of biofilms and to formulate effective biofilm control strategies, researchers in the next decade should recognise that the study of biofilms, i.e. biofilmology, has evolved into a discipline in its own right and that mutual cooperation between the various disciplines towards a multidisciplinary research vision is vital in this field.     

Ranging behavior of Mahale chimpanzees: a 16 year study

We have analyzed the ranging patterns of the Mimikire group (M group) of chimpanzees in the Mahale Mountains National Park, Tanzania. During 16 years, the chimpanzees moved over a total area of 25.2 or 27.4 km², as estimated by the grid-cell or minimum convex polygon (MCP) methods, respectively. Annually, the M group used an average of 18.4 km², or approximately 70 %, of the total home-range area. The chimpanzees had used 80 % of their total home range after 5 years and 95 % after 11 years. M group chimpanzees were observed more than half of the time in areas that composed only 15 % of their total home range. Thus, they typically moved over limited areas, visiting other parts of their range only occasionally. On average, the chimpanzees used 7.6 km² (in MCP) per month. Mean monthly range size was smallest at the end of the rainy season and largest at the end of the dry season, but there was much variability from year to year. The chimpanzees used many of the same areas every year when Saba comorensis fruits were abundant between August and January. In contrast, the chimpanzees used several different areas of their range in June. Here range overlap between years was relatively small. Over the 16 years of the study we found that the M group reduced their use of the northern part of their range and increased their frequency of visits to the eastern mountainous side of their home range. Changes in home-range size correlated positively with the number of adult females but not with the number of adult males. This finding does not support a prediction of the male-defended territory model proposed for some East African chimpanzee unit-groups.     

Cross-cultural comparison of women’s midlife symptom-reporting: a china study

Drawing on ethnographic and survey research conducted by the author in a general population sample in mainland China, this article presents findings on Chinese women’s midlife symptom reporting in comparison with pivotal studies conducted by Lock, Kaufert, and McKinlay in Japan, Canada, and the U.S. Analysis of the China survey data (N = 156 women, age 45–55) reveals for sixteen core symptoms a reporting frequency that is much lower than depicted in classic biomedical models of menopause. At the same time, however, the China data indicates problems with the popular extrapolation that midlife Asian women are virtually symptom-free compared to their North American peers. Finding the Chinese level of symptom-reporting low to moderate depending on the symptom, the article reveals important differences between Chinese and Japanese women in their level and pattern of symptom reporting, as well as substantial overlap with North American women in this regard. Referencing ethnographic materials on Chinese women and the cross-cultural literature on menopause, the article assesses potential explanations for the cross-cultural variation observed, including: local reproductive endocrinology, phytoestrogen consumption, aspects of East Asian culture, the nature of social change, the cultural acceptability of monitoring and voicing symptoms, and differences in dominant conceptions of midlife.     

Reduction of β-thiopyruvic acid by lactate dehydrogenase: a kinetic study

Summary In this paper a steady-state kinetic study on the system lactate dehydrogenase--thiopyruvate--thiolactate is presented and the possible mechanistic and physiological implications are discussed.At pH 7.4 the equilibrium between -thiopyruvate and -thiolactate, in the presence of NADH and lactate dehydrogenase is largerly shifted towards the formation of -thiolactate as in the case of pyruvate and lactate. This can be relevant in connection with the mixed disulfide between cysteine and -thiolactate that is observed to be present in the mammalian body fluids.The catalytic mechanism is of the bi-bi compulsory order type, and rapid equilibrium conditions for the binding of the first substrate (NADH) are shown to apply. A complex inhibition pattern of inhibitions by both substrates, however, prevents simple suggestions about the nature of the dead-end species involved.Abbreviations TPA -thiopyruvic acid - TLA -thiolactic acid - E enzyme This work is gratefully dedicated to Prof. Alessandro Rossi Fanelli on the occasion of his 75th birthday.     

Allosteric regulation of glycogen synthase kinase 3β: a theoretical study

Glycogen synthase kinase 3β (GSK-3β) is a serine-threonine kinase belonging to the CMGC family that plays a key role in many biological processes, such as glucose metabolism, cell cycle regulation, and proliferation. Like most protein kinases, GSK-3β is regulated via multiple pathways and sites. We performed all-atom molecular dynamics simulations on the unphosphorylated and phosphorylated unbound GSK-3β and the phosphorylated GSK-3β bound to a peptide substrate, its product, and a derived inhibitor. We found that GSK-3β autophosphorylation at residue Tyr(216) results in widening of the catalytic groove, thereby facilitating substrate access. In addition, we studied the interactions of the phosphorylated GSK-3β with a substrate and peptide inhibitor located at the active site and observed higher affinity of the inhibitor to the kinase. Furthermore, we detected a potential remote binding site which was previously identified in other kinases. In agreement with experiments we observed that binding of specific peptides at this remote site leads to stabilization of the activation loop located in the active site. We speculate that this stabilization could enhance the catalytic activity of the kinase. We point to this remote site as being structurally conserved and suggest that the allosteric phenomenon observed here may occur in the protein kinase superfamily.     

Tyrosine phosphorylation as a conformational switch: a case study of integrin β3 cytoplasmic tail

Reversible protein phosphorylation is vital for many fundamental cellular processes. The actual impact of adding and removing phosphate group(s) is 3-fold: changes in the local/global geometry, alterations in the electrostatic potential and, as the result of both, modified protein-target interactions. Here we present a comprehensive structural investigation of the effects of phosphorylation on the conformational as well as functional states of a crucial cell surface receptor, α(IIb)β(3) integrin. We have analyzed phosphorylated (Tyr(747) and Tyr(759)) β(3) integrin cytoplasmic tail (CT) primarily by NMR, and our data demonstrate that under both aqueous and membrane-mimetic conditions, phosphorylation causes substantial conformational rearrangements. These changes originate from novel ionic interactions and revised phospholipid binding. Under aqueous conditions, the critical Tyr(747) phosphorylation prevents β(3)CT from binding to its heterodimer partner α(IIb)CT, thus likely maintaining an activated state of the receptor. This conclusion was tested in vivo and confirmed by integrin-dependent endothelial cells adhesion assay. Under membrane-mimetic conditions, phosphorylation results in a modified membrane embedding characterized by significant changes in the secondary structure pattern and the overall fold of β(3)CT. Collectively these data provide unique molecular insights into multiple regulatory roles of phosphorylation.     

Thermal stability of chicken brain α-spectrin repeat 17: a spectroscopic study

Spectrin is a rod-like multi-modular protein that is mainly composed of triple-helical repeats. These repeats show very similar 3D-structures but variable conformational and thermodynamical stabilities, which may be of great importance for the flexibility and dynamic behaviour of spectrin in the cell. For instance, repeat 17 (R17) of the chicken brain spectrin α-chain is four times less stable than neighbouring repeat 16 (R16) in terms of ?G. The structure of spectrin repeats has mainly been investigated by X-ray crystallography, but the structures of a few repeats, e.g. R16, have also been determined by NMR spectroscopy. Here, we undertook a detailed characterization of the neighbouring R17 by NMR spectroscopy. We assigned most backbone resonances and observed NOE restraints, relaxation values and coupling constants that all indicated that the fold of R17 is highly similar to that of R16, in agreement with previous X-ray analysis of a tandem repeat of the two domains. However, (15)N heteronuclear NMR spectra measured at different temperatures revealed particular features of the R17 domain that might contribute to its lower stability. Conformational exchange appeared to alter the linker connecting R17 to R16 as well as the BC-loop in close proximity. In addition, heat-induced splitting was observed for backbone resonances of a few spatially related residues including V99 of helix C, which in R16 is replaced by the larger hydrophobic tryptophan residue that is relatively conserved among other spectrin repeats. These data support the view that the substitution of tryptophan by valine at this position may contribute to the lower stability of R17.     

Iron-sulfur clusters of biotin synthase in vivo: a Mössbauer study

Biotin synthase, the enzyme that catalyzes the last step of the biosynthesis of biotin, contains only [2Fe-2S](2+) clusters when isolated under aerobic conditions. Previous results showed that reconstitution with an excess of FeCl(3) and Na(2)S under reducing and anaerobic conditions leads to either [4Fe-4S](2+), [4Fe-4S](+), or a mixture of [4Fe-4S](2+) and [2Fe-2S](2+) clusters. To determine whether any of these possibilities or other different cluster configuration could correspond to the physiological in vivo state, we have used (57)Fe M?ssbauer spectroscopy to investigate the clusters of biotin synthase in whole cells. The results show that, in aerobically grown cells, biotin synthase contains a mixture of [4Fe-4S](2+) and [2Fe-2S](2+) clusters. A mixed [4Fe-4S](2+):[2Fe-2S](2+) cluster form has already been observed under certain in vitro conditions, and it has been proposed that both clusters might each play a significant role in the mechanism of biotin synthase. Their presence in vivo is now another argument in favor of this mixed cluster form.     

Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B

Spontaneous unidirectional, or vectorial, insertion of transmembrane peptides is a fundamental biophysical process for toxin and viral actions. Polytheonamide B (pTB) is a potent cytotoxic peptide with a β^6.3-helical structure. Previous experimental studies revealed that the pTB inserts into the membrane in a vectorial fashion and forms a channel with its single molecular length long enough to span the membrane. Also, molecular dynamics simulation studies demonstrated that the pTB is prefolded in aqueous solution. These are unique features of pTB because most of the peptide toxins form channels through oligomerization of transmembrane helices. Here, we performed all-atom molecular dynamics simulations to examine the dynamic mechanism of the vectorial insertion of pTB, providing underlying elementary processes of the membrane insertion of a prefolded single transmembrane peptide. We find that the insertion of pTB proceeds with only the local lateral compression of the membrane in three successive phases: “landing,” “penetration,” and “equilibration” phases. The free energy calculations using the replica-exchange umbrella sampling simulations present an energy cost of 4.3 kcal/mol at the membrane surface for the membrane insertion of pTB from bulk water. The trajectories of membrane insertion revealed that the insertion process can occur in two possible pathways, namely “trapped” and “untrapped” insertions; in some cases, pTB is trapped in the upper leaflet during the penetration phase. Our simulations demonstrated the importance of membrane anchoring by the hydrophobic N-terminal blocking group in the landing phase, leading to subsequent vectorial insertion.     

β-thymosins and interstitial lung disease: study of a scleroderma cohort with a one-year follow-up

Background

β-thymosins play roles in cytoskeleton rearrangement, angiogenesis, fibrosis and reparative process, thus suggesting a possible involvement in the pathogenesis of systemic sclerosis. The aim of the study was to investigate the presence of thymosins β₄, β₄ sulfoxide, and β₁₀ in bronchoalveolar lavage fluid of scleroderma patients with interstitial lung disease and the relation of these factors with pulmonary functional and radiological parameters.

Methods

β-thymosins concentrations were determined by Reverse Phase-High Performance Liquid Chromatography-Electrospray-Mass Spectrometry in the bronchoalveolar lavage fluid of 46 scleroderma patients with lung involvement and of 15 controls.

Results

Thymosin β_4, β₄ sulfoxide, and β₁₀ were detectable in bronchoalveolar lavage fluid of patients and controls. Thymosin β₄ levels were significantly higher in scleroderma patients than in controls. In addition, analyzing the progression of scleroderma lung disease at one-year follow-up, we have found that higher thymosin β₄ levels seem to have a protective role against lung tissue damage. Thymosin β₄ sulfoxide levels were higher in the smokers and in the scleroderma patients with alveolitis.

Conclusions

We describe for the first time β-thymosins in bronchoalveolar lavage fluid and their possible involvement in the pathogenesis of scleroderma lung disease. Thymosin β₄ seems to have a protective role against lung tissue damage, while its oxidation product mirrors an alveolar inflammatory status.     

Effects of a hydrological protection zone on the restoration of a raised bog: a case study from Northeast-Germany 1997–2008

We investigated the changes of water level and vegetation in a restored cut-over raised bog in response to a hydrological protection zone established around the bog. The restoration began 1997 and techniques involved ditch blocking within and around the bog to stimulate a return to conditions of intact bog ecosystems. In order to monitor the rehabilitation of the raised bog, water levels and vegetation have been recorded since before restoration measures began. The monitoring is ongoing, but an assessment of 15 year’s data (1994–2008) is presented. A hydrological protection zone with continuous high water levels could be established around the raised bog which minimizes the runoff of precipitation. Shortly after the first measures, the water levels increased significantly at all dipwells. Parallel to the increasing water levels a vascular plant species assemblage and a diverse Sphagnum community developed. In particular Sphagnum fimbriatum, S. palustre, S. recurvum and S. squarrosum spread efficiently. The cover of trees decreased significantly because of high water levels and ongoing acidification by Sphagnum spp. The high water levels have stimulated the re-vegetation and the hydrology self-regulation of the acrotelm. The successful regeneration of the acrotelm particularly became apparent in years with below-average precipitations (e.g. 2008), when the water levels in the central parts of the raised bog did not fall back to the low level reached in previous years, which had also remarkably water deficits (e.g. 2003).     

Misconceptions in biology: a meta-synthesis study of research, 2000–2014

Abstract

Teachers need to be aware of biology misconceptions in their classrooms and how to address them. In response, researchers and science educators have suggested and examined effective practices to prevent and ameliorate misconceptions. An extensive review of the literature gives researchers and educators insights into trends, practices, and gaps in the misconceptions research and helps decide which issues to address and why. The current study shares how researchers in Turkey conduct a content analysis of published misconception research in Turkey by using a form. The analysis resulted in a meta-synthesis (thematic content analysis) that inventoried and compared the purposes, research methods, data collection instruments, and findings of the selected publications. Biology educators in other regions of the world can inform their practice by using this instrument and research methods to learn about trends and patterns in misconception research. Researchers will gain insights into effective methods that have been used to examine misconceptions and will be able to identify biology misconceptions that have been under-investigated and need further analysis.     

Dose-finding evaluation of once-daily treatment with olodaterol,a novel long-acting β2-agonist,in patients with asthma: results of a parallel-group study and a crossover study

Background

Olodaterol is a novel, inhaled long-acting β₂-agonist (LABA) with >24-hour duration of action investigated in asthma and chronic obstructive pulmonary disease.

Methods

Two multicentre studies examined the efficacy and safety of 4 weeks’ once-daily (QD) olodaterol (2, 5, 10 and 20 μg, with background inhaled corticosteroids) in patients with asthma. One randomised, double-blind, parallel-group study (1222.6; 296 patients) administered treatment in the morning. Pulmonary function tests (PFTs) were performed pre-dose (trough) and ≤3 hours post-dose (weeks 1 and 2), and ≤6 hours post-dose after 4 weeks; primary end point was trough forced expiratory volume in 1 second (FEV₁) response (change from baseline mean FEV₁) after 4 weeks. A second randomised, double-blind, placebo- and active-controlled (formoterol 12 μg twice-daily) incomplete-block crossover study (1222.27; 198 patients) administered QD treatments in the evening. PFTs were performed over a 24-hour dosing interval after 4 weeks; primary end point was FEV₁ area under the curve from 0–24 hours (AUC_0–24) response (change from study baseline [mean FEV₁] after 4 weeks).

Results

Study 1222.6 showed a statistically significant increase in trough FEV₁ response with olodaterol 20 μg (0.147 L; 95 % confidence interval [CI]: 0.059, 0.234; p = 0.001) versus placebo, with more limited efficacy and no evidence of dose response compared to placebo across the other olodaterol doses (2, 5 and 10 μg). Study 1222.27 demonstrated increases in FEV₁ AUC_0–24 responses at 4 weeks with all active treatments (p < 0.0001); adjusted mean (95 % CI) differences from placebo were 0.140 (0.097, 0.182), 0.182 (0.140, 0.224), 0.205 (0.163, 0.248) and 0.229 (0.186, 0.272) L for olodaterol 2, 5, 10 and 20 μg, respectively, and 0.169 (0.126, 0.211) for formoterol, providing evidence of increased efficacy with higher olodaterol dose. Olodaterol was generally well tolerated, with a few events associated with known sympathomimetic effects, mainly with 20 μg.

Conclusions

The LABA olodaterol has >24-hour duration of action. In patients with asthma, evidence of bronchodilator efficacy was demonstrated with statistically and clinically significant improvements in the primary end point of trough FEV₁ response measured in clinics over placebo for the highest administered dose of 20 μg in Study 1222.6, and statistically and clinically significant improvements versus placebo in FEV₁ AUC_0–24 responses at 4 weeks for all doses tested in Study 1222.27, which also exhibited a dose response. Bronchodilator efficacy was seen over placebo for all olodaterol doses for morning and evening peak expiratory flow in both studies. All doses were well tolerated.

Trial registrations

{"type":"clinical-trial","attrs":{"text":"NCT00467740","term_id":"NCT00467740"}}NCT00467740 (1222.6) and {"type":"clinical-trial","attrs":{"text":"NCT01013753","term_id":"NCT01013753"}}NCT01013753 (1222.27).

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-015-0249-8) contains supplementary material, which is available to authorized users.     

The study of the brain’s organization of creativity: I. Development of a psychological test

This article describes an original psychological test on verbal creative work comprising a number of tasks designed to study the organization of creative processes in human brain with the help of positron emission tomography (PET) and electroencephalography (EEG). When approved in a group of 30 healthy volunteers, the test revealed principal cognitive strategies of performing creative tasks which formed the basis for elaborating criteria for selecting subjects for physiological study. Empirical substantiation of the proposed test showed its validity for the use in the psychophysiological investigation of creative work.     

Influence of lunar phases on suicide: the end of a myth? A population-based study

The hypothesis of lunar influence on suicide remains widespread, despite the fact that little scientific evidence to substantiate it. We conducted a population-based study to assess the influence of the lunar phases on suicides according to age, sex, and chosen method. The study included all suicides in Middle Franconia between 1998 and 2003. From a population-based sample of 3351 events, the files of 3054 suicides (1949 males and 1105 females) were complete for the study variables. Data were categorized by lunar phase, sex, age, and chosen method—“violent” vs. “non-violent” acts. No significant relationship was detected between the full, absent, and moon's interphases and suicide incidence. Nevertheless, there was a weak association between the absent moon and choice of a non-violent suicide method in men aged less than the median of 40.2 yrs. There was no evidence of a relationship between suicide and lunar phase. Some explanations for this phenomenon are discussed.     

Metabolic fate of a high concentration of glutamine and glutamate in rat brain slices: a ¹³C NMR study

This study was performed to analyze the metabolic fate of a high concentration (5 mM) of glutamine and glutamate in rat brain slices and the participation of these amino acids in the glutamine-glutamate cycle. For this, brain slices were incubated for 60 min with [3-13C]glutamine or [3-13C]glutamate. Tissue plus medium extracts were analyzed by enzymatic and 13C NMR measurements and fluxes through pathways of glutamine and glutamate metabolism were calculated. We demonstrate that both substrates were utilized and oxidized at high rates by rat brain slices and served as precursors of neurotransmitters, tricarboxylic acid (TCA) cycle intermediates and alanine. In order to determine the participation of glutamine synthetase in the appearance of new glutamine molecules with glutamine as substrate, brain slices were incubated with [3-13C]glutamine in the presence of methionine sulfoximine, a specific inhibitor of glutamine synthetase. Our results indicate that 36.5% of the new glutamine appeared was glutamine synthetase-dependent and 63.5% was formed from endogenous substrates. Flux through glutamic acid decarboxylase was higher with glutamine than with glutamate as substrate whereas fluxes from α-ketoglutarate to glutamate and through glutamine synthetase, malic enzyme, pyruvate dehydrogenase, pyruvate carboxylase and citrate synthase were in the same range with both substrates.     

Hair cortisol: a parameter of chronic stress? Insights from a radiometabolism study in guinea pigs

Measurement of hair cortisol has become popular in the evaluation of chronic stress in various species. However, a sound validation is still missing. Therefore, deposition of radioactivity in hair and excretion into feces and urine after repeated injection of (3)H-cortisol was studied in guinea pigs (n?=?8). Each animal was given intraperitoneally 243.6?kBq (3)H-cortisol/day on 3 successive days. After the first injection, all voided excreta were collected for 3?days. After the second injection, hair was shaved off the animals' back and newly grown hair was obtained on day 7. Following methanol extraction, radiolabeled and unlabeled glucocorticoid metabolites (GCM) in fecal and hair samples were characterized by high-performance liquid chromatography (HPLC) and enzyme immunoassays (EIA). In feces, maximum radioactivity was reached 8?h (median) post each injection, whereas maxima in urine were detected in the first samples (median 2.5?h). Metabolites excreted into feces (13.3?%?±?3.7) or urine (86.7?%) returned nearly to background levels. HPLC of fecal extracts showed minor variation between individuals and sexes. In hair, small amounts of radioactivity were present. However, two EIAs detected large amounts of unlabeled GCM, including high levels at the position of the cortisol standard; radioactivity was absent in this fraction, demonstrating that (3)H-cortisol was metabolized. Furthermore, large amounts of immunoreactivity coinciding with a radioactive peak at the elution position of cortisone were found. These results show for the first time that only small amounts of systemically administered radioactive glucocorticoids are deposited in hair of guinea pigs, while measurement of large amounts of unlabeled GCM strongly suggests local production of glucocorticoids in hair follicles.