Is cooperative oxygen binding by hemoglobin really understood?

The enormous success of structural biology challenges the physical scientist. Can biophysical studies provide a truly deeper understanding of how a protein works than can be obtained from static structures and qualitative analysis of biochemical data? We address this question in a case study by presenting the key concepts and experimental results that have led to our current understanding of cooperative oxygen binding by hemoglobin, the paradigm of structure function relations in multisubunit proteins. We conclude that the underlying simplicity of the two-state allosteric mechanism could not have been demonstrated without novel physical experiments and a rigorous quantitative analysis.     

Can morphogenesis be understood in terms of physical rules?

Because the morphogenesis of biological systems is not fully understood, researches from various points of view are necessary. The present author has recently made computer simulations with his colleagues to construct branching systems of human organs, such as the lung airway and the liver blood vessels. In the simulations certain rules are assumed to govern bifurcating processes of the systems. These rules are expressed in terms of physical and geometrical concepts, such as minimum energy consumption and uniform filling of branches in the space of organs. Results of computer simulation are quite similar to real structures. However, actual mechanisms of morphogenesis, i.e. effects of genes or proteins, are not considered in these studies. In this article, the present work is discussed in relation to the concept of biological pattern formation by Meinhardt and a recent study by Miura and Shiota on lung growth.     

Why plants grow poorly on very acid soils: are ecologists missing the obvious?

Factors associated with soil acidity are considered to be limiting for plants in many parts of the world. This work was undertaken to investigate the role of the toxicity of hydrogen (H(+)) which seems to have been underconsidered by ecologists as an explanation of the reduced plant growth observed in very acid soils. Racial differences are reported in plant growth response to increasing acidity in the grass Holcus lanatus L. (Yorkshire-fog) and the tree Betula pendula Roth (Silver Birch). Soils and seeds were collected from four Scottish sites which covered a range of soils from acid (organic and mineral) to more base-rich. The sites and their pH (1:2.5 fresh soil:0.01 M CaCl(2)) were: Flanders Moss (FM), pH 3.2+/-0.03; Kippenrait Glen (KP), pH 4.8+/- 0.05; Kinloch Rannoch (KR), pH 6.1+/-0.16; and Sheriffmuir (SMM), pH 4.3+/-0.11. The growth rates of two races of H. lanatus, FM and KP, and three races of B. pendula (SMM, KP and KR) were measured in nutrient solution cultures at pH 2.0 (H. lanatus only), 3.0, 4.0, 5.0, and 5.6. Results showed races from acid organic soils (FM) were H(+)-tolerant while those from acid mineral soils (SMM) were Al(3+)-tolerant but not necessarily H(+)-tolerant. These results confirmed that populations were separately adapted to H(+) or Al(3+) toxicity and this was dependent upon the soil characteristics at their site of collection. The fact of plant adaptation to H(+) toxicity supports the view that this is an important factor in very acid soils.     

The difficult choice of treatment for poorly controlled maturity onset diabetes: tablets or insulin?

Patients with maturity onset diabetes that is poorly controlled on maximal doses of oral hypoglycaemic agents are difficult to treat. A prospective randomised crossover study was performed in 58 predominantly non-obese patients on maximal doses of glibenclamide or metformin, or both, to find out if insulin would improve control or well being. The patients were given daily injections of up to 48 units of highly purified porcine lente insulin. Glycaemic control was improved by 15% or more in only 18 patients; 14 others felt better but their diabetes was no better controlled. Those whose control was improved by insulin could not be distinguished by age, duration of diabetes, body mass index, or their own treatment preference. C peptide concentrations, however, did help predict the response to insulin, the fasting C peptide to glucose ratio being considerably lower in those patients whose control was better on insulin. These findings suggest that a simple insulin regimen does not necessarily lead to better glycaemic control in maturity onset diabetes. Nevertheless, a trial of insulin is often justified since it poses few practical difficulties and makes some patients feel better even if their control is not improved. A more complex regimen might improve control in more cases, but it might also be less acceptable to older patients.     

Screening for celiac disease in poorly controlled type 2 diabetes mellitus: worth it or not?

Background

Recent studies have demonstrated that immune factors might have a role in the pathophysiology of insulin resistance and type 2 diabetes mellitus (T2DM). Inappropriate glycemic control in patients with T2DM is an important risk factor for the occurrence of diabetes complications. The prevalence of celiac disease (CD) is high in type 1 diabetes mellitus however, there are scarce data about its prevalence in T2DM. Our aim was to investigate the prevalence of celiac disease among insulin-using type 2 diabetes patients with inappropriate glycemic control.

Methods

IgA tissue transglutaminase antibodies (tTGA IgA) test was performed as a screening test. A total of 135 patients with T2DM whose control of glycemia is inappropriate (HbAlc value >7%) in spite of using insulin treatment for at least 3-months (only insulin or insulin with oral antidiabetic drugs) and 115 healthy controls were enrolled in the study. Upper gastrointestinal endoscopy with duodenal biopsy was performed to all patients with raised tTGA IgA or selective lgA deficiency.

Results

Gender, age, body mass index (BMI) and tTGA IgA, kreatinin, calcium, LDL-cholesterol (LDL-C), total cholesterol, 25-OH vitamin D₃ levels were similar between groups. Systolic and diastolic blood pressure, waist circumference, fasting plasma glucose, postprandial plasma glucose, urea, sodium, HbA1c, LDL-C, triglyceride, vitamin B12 levels were significantly higher in DM group (p < 0.0001). BMI, high-sensitive CRP, microalbuminuria, and AST, ALT, potassium, phosphorus levels were significantly higher in the T2DM group (p < 0.05). HDL-cholesterol and parathormone levels were significantly lower in the T2DM group (p < 0.05). Two of the 135 patients with T2DM were diagnosed with CD (1.45%).

Conclusions

The prevalence of celiac disease among patients with type 2 diabetes, with poor glycemic control despite insulin therapy, is slightly higher than the actual CD prevalence in general population. Type 2 diabetic patients with inappropriate control of glycemia in spite of insulin treatment might be additionally tested for Celiac disease especially if they have low C-peptide levels.

     

Is the molecular basis of metronidazole resistance in microaerophilic organisms understood?

Metronidazole is an antibiotic that has been effective against many microaerophilic microorganisms with importance in medicine and animal husbandry. The development of increasing resistance against current treatments by many of these organisms has created an urgent need to establish the molecular bases of resistance, knowledge which will help to develop novel diagnostic methods and identify new therapeutic targets. Significant progress has been made in understanding resistance to this antibiotic in the human pathogens Helicobacter pylori and, to a lesser extent, Campylobacter spp. However, insufficient knowledge of the physiology and genetics of these and other related bacteria has led to investigations based on hypotheses that themselves must be established more thoroughly. This review presents the status of our current knowledge of metronidazole resistance and outlines reasons to explain some of the conflicting evidence and controversy in the interpretation of results in this area.     

Origin and hidden diversity within the poorly known Galápagos snake radiation (Serpentes: Dipsadidae)

Galápagos snakes are among the least studied terrestrial vertebrates of the Archipelago. Here, we provide a phylogenetic analysis and a time calibrated tree for the group, based on a sampling of the major populations known to occur in the Archipelago. Our study revealed the presence of two previously unknown species from Santiago and Rábida Islands, and one from Tortuga, Isabela, and Fernandina. We also recognize six additional species of Pseudalsophis in the Galápagos Archipelago (Pseudalsophis biserialis from San Cristobal, Floreana and adjacent islets; Pseudalsophis hoodensis from Española and adjacent islets; Pseudalsophis dorsalis from Santa Cruz, Baltra, Santa Fé, and adjacent islets; Pseudalsophis occidentalis from Fernandina, Isabela, and Tortuga; Pseudalsophis slevini from Pinzon, and Pseudalsophis steindachneri from Baltra, Santa Cruz and adjacent islets). Our time calibrated tree suggests that the genus Pseudalsophis colonized the Galápagos Archipelago through a single event of oceanic dispersion from the coast of South America that occurred at approximately between 6.9?Ma and 4.4?Ma, near the Miocene/Pliocene boundary.www.zoobank.org/urn:lsid:zoobank.org:pub:2679FD19-01E5-48FE-A0DA-A88FF145DE56     

Fine needle aspiration of poorly differentiated oxyphilic (Hürthle cell) thyroid carcinoma: a case report

BACKGROUND: Poorly differentiated oxyphilic (Hürthle cell) carcinomas are a more recently described variant of poorly differentiated thyroid carcinoma and are characterized by a prominent Hürthle cell component in a solid or trabecular arrangement. Clinically, poorly differentiated oxyphilic carcinomas behave more aggressively as compared to classic Hürthle cell carcinomas, which have a predominantly follicular pattern. Although the histology of these rare thyroid tumors has been reported in the literature, the cytologic features on fine needle aspiration biopsy have not been described before. CASE: A 73-year-old man with a long history of radioactive iodine and levothyroxine therapy for multinodular goiter presented with a painful, rapidly expanding, 6-cm, left thyroid mass with aggressive radiologic features. Fine needle aspiration biopsy of the mass yielded extremely cellular smears with a dual population of medium-sized follicular cells and numerous Hürthle cells. Subsequent thyroidectomy confirmed the malignant nature of this Hürthle cell-rich tumor, warranting a diagnosis of poorly differentiated oxyphilic (Hürthle cell) thyroid carcinoma. CONCULSION: Poorly differentiated oxyphilic thyroid carcinoma is an aggressive variant of Hürthle cell carcinomas and must enter the differential diagnosis when fine needle aspiration biopsy of a radiologically aggressive thyroid mass yields extremely hypercellular smears with a prominent Hürthle cell component.     

Accumulation of anthracotic particles along lymphatics of the human lung: Relevance to “hot spot” formation after inhalation of poorly soluble radionuclides

Summary Large lung sections of humans of advanced adult age revealed a markedly nonuniform retention pattern of dense anthracotic particle aggregates, with an impressive accumulation of this material along pulmonary lymphatics, i.e. the deep (peribronchial), septal (perivenous) and superficial (pleural) networks. Conversely, the alveolar parenchyme contained only occasional, small aggregates of macrophages heavily loaded with carbon, representing little more than 2% of this material in lung tissue. Although translocation kinetics of anthracotic particles cannot readily be compared to those of highly toxic -emitting, poorly soluble radionuclides such as²³⁹PuO₂, lymphatic drainage of the latter over the years may also be expected to lead to a concentration of radioactive material along lymph vessels. Since human data on the effects of inhaled²³⁹PuO₂ are virtually lacking, the above distribution pattern is apt to help in identifying cells and other tissue components most heavily at risk. Findings are also relevant to the problem of hot spot formation in vivo and its possible sequelae. The latter are briefly discussed with regard to both stochastic and non-stochastic effects.Dedicated to Prof. L.E. Feinendegen on the occasion of his 60th birthday     

Just another island dwarf? Phenotypic distinctiveness in the poorly known Soemmerring's Gazelle,Nanger soemmerringii (Cetartiodactyla: Bovidae), of Dahlak Kebir Island

The gazelles of Dahlak Kebir are the only population of Nanger soemmerringii Cretzschmar, 1828 living on an island. Little is known on the biology of these animals, except that they are evidently smaller than their conspecifics living on the continent. We took advantage of a recently acquired collection of crania, probably the largest available study sample of the Dahlak Kebir population worldwide, to explore the phenotypic variation of this island endemism. To this aim, we employed state of the art geometric morphometrics techniques and multivariate statistics to compare the insular population with samples of two out of three subspecies of N. soemmerringii from continental Africa. We found that not only is the size of the animal remarkably smaller in Dahlak Kebir gazelles, but their cranial shape is also highly distinctive, and this might be only partly explained by allometry. We also showed that phenotypic variance might have been reduced in the island population, likely as a consequence of genetic bottlenecks. This unique population is part of a species vulnerable to extinction. Our results suggest that the Dahlak Kebir Island gazelles might represent a significant component of its variation and potential for adaptive change and evolution. More information, including molecular data, and an accurate assessment of its taxonomic relevance and conservation status, is urgently needed. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 603–620.     

Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry.

This paper examines whether the in vivo behavior of yeast glycolysis can be understood in terms of the in vitro kinetic properties of the constituent enzymes. In nongrowing, anaerobic, compressed Saccharomyces cerevisiae the values of the kinetic parameters of most glycolytic enzymes were determined. For the other enzymes appropriate literature values were collected. By inserting these values into a kinetic model for glycolysis, fluxes and metabolites were calculated. Under the same conditions fluxes and metabolite levels were measured. In our first model, branch reactions were ignored. This model failed to reach the stable steady state that was observed in the experimental flux measurements. Introduction of branches towards trehalose, glycogen, glycerol and succinate did allow such a steady state. The predictions of this branched model were compared with the empirical behavior. Half of the enzymes matched their predicted flux in vivo within a factor of 2. For the other enzymes it was calculated what deviation between in vivo and in vitro kinetic characteristics could explain the discrepancy between in vitro rate and in vivo flux.     

New observations on some poorly known protasterid ophiuroids from the Lower Devonian Hunsrück Slate of Germany

Four genera and species of protasterid ophiuroids have been reported from the Lower Devonian Hunsrück Slate:Bundenbachia beneckei, Palaeophiomyxa grandis, Mastigophiura grandis, andPalaeophiura simplex. In addition, the speciesMiospondylus rhenanus has traditionally been recognized as a member of the Lapworthuridae, a group of ophiuroids with paired but unfused ambulacrals. This ambulacral arrangement would make it unique among Hunsrück Slate ophiuroids.Palaeophiura simplex andM. rhenanus were originally based on Single, poorly preserved specimens, and their morphology has remained poorly understood. A restudy of the type material offP. simplex andM. rhenanus and a detailed comparison to other Hunsrück ophiuroids warrants reassignment of these taxa toBundenbachia beneckei.Palaeophiura simplex is a juvenile example of this species andM. rhenanus is a peculiarly preserved adult. A newly prepared, well-preserved specimen ofBundenbachia beneckei expands our knowledge of the morphology of its mouthframe. In addition,Mastigophiura grandis is revised and redescribed based on newly recognized fossil material.     

Acquisition of phosphorus and other poorly mobile nutrients by roots. Where do plant nutrition models fail?

Background

In the context of increasing global food demand, ecological intensification of agroecosystems is required to increase nutrient use efficiency in plants while decreasing fertilizer inputs. Better exploration and exploitation of soil resources is a major issue for phosphorus, given that rock phosphate ores are finite resources, which are going to be exhausted in decades from now on.

Scope

We review the processes governing the acquisition by plants of poorly mobile nutrients in soils, with a particular focus on processes at the root?Csoil interface. Rhizosphere processes are poorly accounted for in most plant nutrition models. This lack largely explains why present-day models fail at predicting the actual uptake of poorly mobile nutrients such as phosphorus under low input conditions. A first section is dedicated to biophysical processes and the spatial/temporal development of the rhizosphere. A second section concentrates on biochemical/biogeochemical processes, while a third section addresses biological/ecological processes operating in the rhizosphere.

Conclusions

New routes for improving soil nutrient efficiency are addressed, with a particular focus on breeding and ecological engineering options. Better mimicking natural ecosystems and exploiting plant diversity appears as an appealing way forward, on this long and winding road towards ecological intensification of agroecosystems.     

Small mammal diversity of a poorly known and threatened Amazon region,the Tapajós Area of Endemism

Biodiversity and Conservation - The Amazon region is a mosaic of distinct areas of endemism (AoE), each with its evolutionary relationships and biotic assemblages. Among them, the Tapajós AoE...     

Solubilization of poorly water-soluble bioactive molecules in neutral aqueous media by complexation with renatured β-1,3-1,6-glucan nanoparticles

The design of scaffolds for solubilizing/dispersing poorly water-soluble bioactive molecules in neutral aqueous media is a major challenge of functional food, pharmaceuticals, and cosmetics development, as highlighted by the plethora of corresponding solubilization/dispersion strategies. Herein, renatured β-1,3-1,6-glucan (r-glucan) nanoparticles prepared by neutralization of alkali-denatured β-1,3-1,6-glucan and subsequent centrifugation are used as a host to disperse water-insoluble bioactive molecules (curcumin, all-trans-retinoic acid, and rebamipide) by simple mixing of host and guest solutions. Curcumin in the r-glucan cavity is found to be stacked in the form of J-aggregates and twisted along the helix, and is demonstrated to be retained for significantly longer than curcumin in the corresponding γ-cyclodextrin (γ-CD) complex. Specifically, curcumin incorporated in γ-CD is released within 5.5 hours, whereas that in the r-glucan complex is released very slowly, with 12% of curcumin in the latter complex retained after 31-day incubation at 37°C. Thus, inclusion protocol simplicity and slow release ability make r-glucan nanoparticles a potential carrier scaffold for various applications.     

Aerobic mineralization of 4,4′-dichlorobiphenyl and 4-chlorobenzoic acid by a novel natural bacterial strain that grows poorly on benzoate and biphenyl

Achromobacter xylosoxidans strain IR08 was isolated from soil contaminated with electrical transformer fluid by enrichment culture containing Aroclor 1221 as the sole carbon source. This strain was found to grow on all monochlorobiphenyls, 4,4′-dichlorobiphenyl (4,4′-diCB) and a wide range of other xenobiotic compounds. During growth on 4,4′-diCB, a near-stoichiometric amount of chloride was excreted into the culture fluid in less than 5 days and growth yield was more than twice that achieved on biphenyl. The production of 4-CBA or chlorocatechol as a metabolite was not observed. Quite unusually, coincubation of strain IR08 with 4,4′-diCB and biphenyl at relatively equal concentrations showed preferential utilization of the chlorobiphenyl: 4,4′-diCB was mineralized in less than 5 days concomitant with stoichiometric release of chloride, while biphenyl was poorly degraded. Growth on 2.5 mM CBA also resulted in complete disappearance of the substrate, however, inorganic chloride recovered from the culture broth was less than 65%. The isolation of a dichlorobiphenyl-mineralizing rather than transformation strain such as IR08 is an important advance in an effort to develop effective bioremediation strategy for polychlorinated biphenyl-contaminated soil.     

Light chain subunit of a poorly soluble human IgG2λ crystallizes in physiological pH environment both in cellulo and in vitro

Prominent inclusion bodies can develop in the endoplasmic reticulum (ER) when overexpressed antibodies possess intrinsically high condensation propensities. These observations suggest that antibodies deemed to show notable solubility problems may reveal such characteristics preemptively in the form of ER-associated inclusion bodies during antibody overexpression. To define the relationships between solubility problems and inclusion body phenotypes, we investigated the biosynthesis of a model human IgG2λ that shows severe opalescence in an acidic formulation buffer yet retains high solubility at physiological pH. Consistent with the pH-dependent solubility characteristics, the model antibody did not induce notable inclusion body in the physiological pH environment of the ER lumen. However, when individual subunit chains of the antibody were expressed separately, the light chain (LC) spontaneously induced notable crystal-like inclusion bodies in the ER. The LC crystallization event was readily reproducible in vitro by simply concentrating the purified LC protein at physiological pH. Two independent structural determinants for the LC crystallization were identified through rational mutagenesis approach by monitoring the effect of amino acid substitutions on intracellular LC crystallogenesis. The effect of mutations on crystallization was also recapitulated in vitro using purified LC proteins. Importantly, when introduced directly into the model antibody, a mutation that prevents the LC crystallization remediated the antibody's solubility problem without compromising the secretory output or antigen binding. These results illustrate that the ER can serve as a “physiological test tube” that not only reports secretory cargo's high condensation propensity at physiological pH, but also provides an orthogonal method that guides antibody engineering strategy.