Exterior Branch Research Articles

Genome Evolution of Filamentous Cyanobacterium Nostoc Species: From Facultative Symbiosis to Free Living.

In contrast to obligate bacteria, facultative symbiotic bacteria are mainly characterized by genome enlargement. However, the underlying relationship of this feature with adaptations to various habitats remains unclear. In this study, we used the global genome data of Nostoc strains, including 10 novel genomes sequenced in this study and 26 genomes available from public databases, and analyzed their evolutionary history. The evolutionary boundary of the real clade of Nostoc species was identified and was found to be consistent with the results of polyphasic taxonomy. The initial ancestral species of Nostoc was demonstrated to be consistent with a facultative symbiotic population. Further analyses revealed that Nostoc strains tended to shift from facultative symbiosis to a free-living one, along with an increase in genome sizes during the dispersal of each exterior branch. Intracellular symbiosis was proved to be essentially related to Nostoc evolution, and the adaptation of its members to free-living environments was coupled with a large preference for gene acquisition involved in gene repair and recombination. These findings provided unique evidence of genomic mechanisms by which homologous microbes adapt to distinct life manners and external environments.

Methods for reducing the number of sequences in molecular evolutionary analyses

Due to the progress in the sequencing technology, the number of nucleotide sequences for pathogens deposited in the public databases has been increasing rapidly. Consequently, in the molecular evolutionary analyses of pathogens, it may occasionally be difficult to include all the available sequences and necessary to reduce the number of sequences to accomplish computation within a realistic time frame. Here several methods for reducing the number of sequences were evaluated using the amount of evolutionary information contained in the retained sequences, which was measured as the total branch length of the phylogenetic tree (L). In the REA (random elimination in alignment) method, each of sequences was eliminated with equal probability. In the phylogenetic tree-based methods, the sequences associated with short exterior branches were eliminated; the sequences to be eliminated were required to constitute neighbors with another sequence in the CNT (closest neighbor in tree) method, whereas no such restriction was imposed in the SET (shortest exterior branch in tree) method. In the distance matrix-based methods, the sequences with small average distances to other sequences were eliminated; the sequences to be eliminated were required to be closely related to another sequence in the CPM (closest pair in matrix) method, whereas no such restriction was imposed in the SDM (smallest average distance in matrix) method. From the analyses of 2113 sequences for viral protein 1 of norovirus and 13,063 sequences for hemagglutinin of influenza A virus, it was observed that the CPM method was the most useful to obtain large L, in which the exterior branch length (LE) tended to be elongated. In contrast, the interior branch length (LI) tended to be elongated such that the LI/LE was heightened in the SDM method, which may be suitable for the phylogenetic analysis. The nucleotide diversity (π), the synonymous diversity (πS), the nonsynonymous diversity (πN), and the πN/πS were almost constant in the REA method, whereas they increased in other methods, suggesting that the REA method may be appropriate for the analyses of population diversity and natural selection.

Impressions on the Evolution of Naturalism: Interiority, Exteriority, and the International/Interdisciplinary Nature of Naturalism

Naturalism, as a movement and genre, was heavily influenced by the work of Émile Zola, particularly by his essay, Le roman expérimental (1880). However, despite Zola’s strong influence, Naturalism was also significantly influenced by the ideas of others that go beyond and even predate those of Zola. As a result, Naturalism is generally accepted as having originated in France in the late 19th century, and having extended into the early 20th century, however it soon became an international as well as an interdisciplinary movement and genre. More specific examples of this international and interdisciplinary network of Naturalism can be seen in the writing of Zola, Joris-Karl Husymans, and Oscar Wilde, as well as the painting of Cécile Douard, Vincent van Gogh, Gustave Caillebotte, and Claude Monet. Furthermore, these examples reveal that Naturalism evolved into a more interior branch, as well as a more exterior branch, and they also reveal some strong evolutionary links between not only Naturalism and Impressionism, but also between Naturalism and Decadence/Aestheticism. These latter links have seen little discussion in relation to Naturalism, particularly on the basis of the roles that interiority and exteriority play in the international and interdisciplinary expressions of Naturalism.

PREVENTION OF YATROGENIC DAMAGES OF THE LARYNGEAL NERVES IN TRADITIONAL AND MINIMALLY INVASIVE THYROID SURGERY

Objective. To assess the effectiveness of using the intraoperative neuromonitoring for conventional and minimally invasive surgical interventions on the thyroid gland for the prevention of the laryngeal nerve damage. Material and methods. For achieving this goal it was performed the retrospective analysis of surgical treatment of 310 patients with thyroid gland diseases, and 54 patients were selected, which were divided into 2 groups matched by sex and age, the nature of thyroid pathology and volume of surgical intervention: in the first (main, n = 27) operations were carried out using intraoperative neuromonitoring, in the second (control, n = 27) - visual monitoring of the laryngeal nerves was performed. The survey was performed according to the Russian and international clinical guidelines. Laryngoscopy was performed for all patients before operation and for patients with impaired phonation function - after it. «NIM-Neuro® 3.0» device with special armored endotracheal tubes preloaded with circular (detecting), as well as stimulating electrodes for searching and continuous monitoring of laryngeal nerves was used for intraoperative neuromonitoring during the operation. Results of the study. Traditional interventions were conducted on the 6 patients, minimally invasive nonendoscopic surgical - on 25, video-assisted - on 23. The exterior branch of the superior laryngeal nerve has found in 25 (92.6%) patients of the main group and 8 of the (29.6%) control group. Recurrent laryngeal nerve was identified in 27 (100%) patients of the 1st group and in 26 (96.3%) patients of the 2nd group by visual inspection. In the main group there are no cases of intraoperative fixation of the loss or signal attenuation during the laryngeal nerves monitoring, which is proved by the absence of single- and double-sided paresis of the larynx in the postoperative period. Only in 2 patients there was functional dysphonia on hypotonic type. In the control group the laryngeal dysfunction in the form of functional dysphonia (n = 1), paresis (n = 1) and paralysis (n = 1) has occurred in 3 patients. Conclusion. It has been found out that intraoperative neuromonitoring is an effective additional method of neural structures detecting, and it does not substitute the anatomic visualization of laryngeal nerves. intraoperative neuromonitoring in patients with high risk of complications (repeated operations on the thyroid gland, thyroid cancer with extrathyroidal proliferation and regional metastases) can reduce the incidence of paresis and paralysis of the larynx. All minimally invasive interventions on the thyroid gland should be accompanied by the intraoperative neuromonitoring of laryngeal nerves (8 figs, 1 table, bibliography: 15 refs).

Management of the exterior branch of the superior laryngeal nerve among thyroid surgeons – Results from a nationwide survey

IntroductionThe external branch of the superior laryngeal nerve is important for the voice. However, it is unknown how thyroid surgeons manage this nerve during operations. We hypothesised that this management is related to the surgeon's age, gender, the surgeons' annual number of thyroid operations, i.e volume, and surgical specialisation. MethodsWe sent a 17-item enquiry by e-mail to members of the Swedish Endocrine Surgical Society and the Swedish Association for Otorhinolaryngology – Head and Neck Surgery. The questions covered subjects such as age, gender, type of department and operation volume of the surgeon, and whether and how the surgeon would try to preserve and/or identify the EBSLN during an operation. Surgeons were asked to rate the importance of the nerve, and of their use of laryngoscopy and/or voice recording. ResultsThere were 85 respondents. Ninety per cent of them would always or often try to preserve the nerve, but only half would always or often try to identify it. Endocrine surgeons more often stated that they would preserve the nerve; they rated its importance more highly and they more often mentioned the use of neuromonitoring to identify the nerve, than head and neck surgeons. Head and neck surgeons on the other hand were more likely to perform laryngoscopy. Endocrine surgeons more often performed >50 thyroid operations per year than head and neck surgeons. ConclusionsManagement of the external branch of the superior laryngeal nerve differed according to surgeon specialisation, which in turn was associated with surgical volume.

EXTRACAPSULAR TOTAL THYROIDECTOMY IN THE BENIGN THYROID DISEASE

EXTRACAPSULAR TOTAL THYROIDECTOMY IN THE BENIGN THYROID DISEASE (Abstract): The extracapsular total thyroidectomy is the surgical technique for the monobloc resection of the thyroid parenchyma, between the Charpy fascia and the thyroid gland’s own capsule with the preservation of the recurrent nerve, parathyroids, and the exterior branch of the superior laryngeal nerve. Even though this technique represents the treatment of choice in the case of malignant thyroid lesions (in association with the lateral or central compartment lymphadenectomy or not), its indication has been extended in the presence of a benign cytology (FNAB – Bethesda II, III) associated with lesions disseminated in the entire thyroid parenchyma. The intracapsular total thyroidectomy, the subtotal thyroidectomy and the Dunhill operation are surgical techniques also indicated in the case of benign multinodular thyroid lesions disseminated in the entire parenchyma. The aim of this video documentary is to illustrate the extracapsular total thyroidectomy in the benign thyroid disease. Different procedures key points are highlighted: operating room set up, the regional bilateral superficial cervical plexus anaesthesia with the aim of reducing post-operatory pain, the left lateral surgical approach of the left thyroid lobe, and the superior polar approach of the right thyroid lobe respectively, the extracapsular monobloc resection of the thyroid parenchyma spearing the recurrent nerve and the parathyroids, the dissection of the James-Berry ligament, drainage and closure of the musculofascial plans and the wound. Even the indication of extracapsular total thyroidectomy in the case of benign thyroid lesions is still controversial, this technique reduces the risk of recurrent and parathyroid complications and, the risk to develop tumors on the remnant thyroid parenchyma.

Branch Lengths on Birth–Death Trees and the Expected Loss of Phylogenetic Diversity

Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where pendant branches leading to tips can be very short compared with branches deeper in the tree. Here, we analyze alternative and more realistic Yule and birth-death models. We show how censoring at the present both makes average branches one half what we might expect and makes pendant and interior branches roughly equal in length. Although dependent on whether we condition on the size of the tree, its age, or both, these results hold both for the Yule model and for birth-death models with moderate extinction. Importantly, the rough equivalency in interior and exterior branch lengths means that the loss of evolutionary history with loss of species can be roughly linear. Under these models, the Tree of Life may offer limited redundancy in the face of ongoing species loss.

A phylogenetic approach to detecting reassortments in viruses with segmented genomes

When multiple strains of viruses with segmented genomes co-infect a single cell, strains with novel genomic constellations may be created. This mutational process, called reassortment, has caused pandemics of influenza A virus in 1957 and 1968. Here a phylogenetic approach to detecting reassortments, which can be used even when the phylogenetic tree constructed for all strains analyzed is unreliable, is presented. A quartet of strains is examined at a time, where a phylogenetic tree is constructed for each genomic segment and the topology is compared among segments only when all quartet trees are supported with a statistical significance. The occurrence of reassortment and the segments involved in the reassortment event are inferred according to the pattern of topological difference among segments. The reassortment point for a pattern is inferred by superimposing the exterior branches of relevant quartet trees on the all-strains trees. In the analysis of H1N1 and H3N2 human influenza A viruses, a topological difference was observed for all pairs of genomic segments, suggesting that there is no pair of segments that has always co-segregated in reassortment during the evolutionary history of these viruses. When the reassortment point was inferred for the pattern of topological difference that was supported with the largest number of quartets for each virus, the results appeared to be mostly correct, suggesting that the method was largely reliable.

Microscopic anatomy of nevers and blood vessels of the finger distal phanlanx and its clinical significance

Objective To provide anatomical evidence for the repair of wounds of finger distal phalanx,espe-cially for the recovery of feeling. Methods 10 samples of fresh adult hand were dissected under microscope. The course,branches,distribution and external diameter of nerves and blood vessels in finger distal phalanx and morpho-logical relationship between nerves and vessels were measured. Results Proper palmar digital nerves mostly step over digital arteries at section starts of distal finger arterial arcades and go to finger pulps and latero-backs. Their thinks di-vide into 2 branches. Transverse diameters of interior and exterior branches are 0.8 ～ 1.2 mm and 0.9 ～ 1.4 mm re-spectively at liner semilunaris levels. Distributionsof left and right branches are reciprocal chiasmas. Conclusion Finger nerve mostly ramifies to finger pulp,finger tip and finger back at the level of phalangette bottom. Its branches are lower and thinner than concomitant arteries. The suitable anatomy region for anastomosis of nerves and blood ves-sels is the middle1/3 section from the distal interphalangeal joint to the nail during replanation of amputated finger pa-ratelum. Key words: Fingers; Microdissection

Medical diagnostic ultrasound system and method for flow analysis

Medical diagnostic ultrasound methods and systems for automated flow analysis are provided. Multiple cross-sectional areas along a vessel are determined automatically. A processor locates an abnormality as a function of the multiple cross-sectional areas, such as identifying a cross-sectional area that is a threshold amount less than an average cross-sectional area. The abnormal area is highlighted on the display to assist with medical diagnosis. For the carotid artery, the interior and exterior branches are labeled to assist medical diagnosis. The two branches are automatically identified. The branch associated with additional small branches is identified as the exterior carotid.

Photo-acclimation dynamics of the coral Stylophora pistillata to low and extremely low light

Photo-acclimation dynamics of the symbiotic coral Stylophora pistillata to lowering light intensities in the range of 95% to 0.8% of incident surface photosynthetic active radiation (PAR 0) was studied. Coral colonies were sampled from 1- to 2-m depths in open and shaded habitats from the fringing reef of Sesoko Island (near the Tropical Biosphere Research Center, University of the Ryukyus) Okinawa, Japan. Photo-acclimation of exterior branches of coral colonies were examined in outdoor aquarium, where light regime and feeding were similar to field conditions. Two photo-acclimation reactions were studied: (1) changes in chlorophyll concentrations in zooxanthellae; (2) changes in zooxanthellar population density in coral branches. In parallel, we measured an average volume of zooxanthellae, proliferating zooxanthellae frequency (PZF) and degrading zooxanthellae frequency (DZF). It was shown that the coral S. pistillata can survive and acclimate to a wide range of light intensities from 95% to 0.8% PAR 0. Acclimation to low light (30% and 8% PAR 0) involves maximizing the light harvesting capacity by increasing photosynthetic pigment concentration in zooxanthellae and zooxanthellar population density in coral branches. Under extremely low light (0.8% PAR 0), the coral lost zooxanthellae by degradation (perhaps digestion) and retained zooxanthellae-accumulated high concentrations of chlorophyll. The photo-acclimation process is dynamic and immediate. Changes in pigment concentrations in zooxanthellae occurred within 2–4 days and changes in zooxanthellar population densities occurred within 40 days. Zooxanthellae population densities were regulated by changes in rates of division and degradation of symbiotic cells.

Quartet-Mapping, a Generalization of the Likelihood-Mapping Procedure

Likelihood-mapping (LM) was suggested as a method of displaying the phylogenetic content of an alignment. However, statistical properties of the method have not been studied. Here we analyze the special case of a four-species tree generated under a range of evolution models and compare the results with those of a natural extension of the likelihood-mapping approach, geometry-mapping (GM), which is based on the method of statistical geometry in sequence space. The methods are compared in their abilities to indicate the correct topology. The performance of both methods in detecting the star topology is especially explored. Our results show that LM tends to reject a star tree more often than GM. When assumptions about the evolutionary model of the maximum-likelihood reconstruction are not matched by the true process of evolution, then LM shows a tendency to favor one tree, whereas GM correctly detects the star tree except for very short outer branch lengths with a statistical significance of >0.95 for all models. LM, on the other hand, reconstructs the correct bifurcating tree with a probability of >0.95 for most branch length combinations even under models with varying substitution rates. The parameter domain for which GM recovers the true tree is much smaller. When the exterior branch lengths are larger than a (analytically derived) threshold value depending on the tree shape (rather than the evolutionary model), GM reconstructs a star tree rather than the true tree. We suggest a combined approach of LM and GM for the evaluation of starlike trees. This approach offers the possibility of testing for significant positive interior branch lengths without extensive statistical and computational efforts.

Effects of dissolved ammonium addition and host feeding with Artemia salina on photoacclimation of the hermatypic coral Stylophora pistillata

Effects of nutrient treatments on photoacclimation of the hermatypic coral Stylophora pistillata (Esper) were studied. Studies on photoacclimation of colonies from different light regimes in the field were evaluated and used to design laboratory experiments. Coral colonies were collected in the Gulf of Eilat (Israel) from January to March 1993. Exterior branches of colonies from different depths (1 to 40 m) displayed different trends in production characteristics at reduced and very low levels of illumination. From 24 ± 3% to 12 ± 2% of incident surface photosynthetic active radiation (PARo), zooxanthella population density and chlorophyll a+c per 106 zooxanthellae increased, a trend seen in the range of light levels optimal for coral growth (90 to 30% PARo). The Pmax of CO2 per 106 zooxanthellae decreased, while Pmax of CO2 per 103 polyps increased, indicating an increase in zooxanthella population density at low light levels. Proliferous zooxanthella frequency (PZF, a measure of zooxanthella division) declined significantly at light levels <18 ± 3% PARo. At the lowest levels of illumination (<5% PARo), zooxanthella population density decreased, as did the PZF; chl a+c per 106 zooxanthellae was unchanged. In 28-d experiments, exterior coral branches from the upper surfaces of colonies from 3 m depth (65 ± 4% PARo) were incubated in aquaria under bright (80 to 90% PARo), reduced (20 to 30% PARo), and extremely low (2 to 4% PARo) light intensities. At each light intensity, the corals were maintained in three feeding treatments: sea water (SW); ammonium enriched SW (SW + N); SW with Artemia salina nauplii (SW + A). An increase in Pmax of CO2 per 103 polyps was found in corals acclimated to reduced light (20 to 30% PARo) in nutrient-enriched SW, while in SW, where the increase in zooxanthella population density was smaller, it did not occur. Nutrient enrichments (SW + N at 2 to 4% PARo and SW + A at 20 to 30% PARo) increased zooxanthella population density, but had no effect on chl a+c per 106 zooxanthellae. Acclimation for 14 d to reduced (10 to 20% PARo) and extremely low (1 to 3% PARo) light intensities shifted 14C photoassimilation into glycerol and other compounds (probably glycerides), rather than sugars. Both ammonium addition and feeding with Artemia salina nauplii resulted in an increase in photosynthetic assimilation of 14C into amino acids. We conclude that acclimation to reduced light consists of two processes: an increase in photosynthetic pigments and in zooxanthella population density. Both processes require nitrogen, the increase in zooxanthella population density needing more; this adaptation is therefore limited in nitrogen-poor sea water.

Starch Biosynthesis. 3: The Glycogen Precursor Mechanism Using Phosphorylase in the Production of the Precursor Glycogen

Based on the previously proposed glycogen precursor mechanism (S. R. Erlander, Enzymologia 19 (1958), 273–283), it is now proposed that phosphorylase is the primary enzyme for the production of linear chains in the precursor glycogen. The mechanism involves the translocation of ADPglucose (ADPGlu), and is suppressed by ATP because of a reverse of the ADPglucose pyrophosphorylase (ADPG pp) mechanism. Soluble starch synthase II (SSS II) is a back-up system, involves the translocation of glucose-6-phosphate (Glu-6-P), and is activated, not suppressed, by ATP, and is used if phosphorylase or the ADPGlu translocator is destroyed. Each system is independent and produces products which suppress the other. Hence, only one system works at a time. Both mechanisms produce a glycogen precursor and both are dependent upon ADPGlu pp. The initial higher radioactivity of amylose and the constant yield of amylose can be explained by a three or four day biosynthesis of this glycogen, followed by the removal of the glycogen's exterior branches by debranching enzymes to produce amylose and amylopectin. These removed branches are first degraded (using SSS I and II) to ADPGlu, which is the only source of ADPGlu for amylose synthesis. The retention of the polymodal behavior of debranched amylopectin in going from Bomi to shx barley amylopectins is most likely due to a change from phosphorylase to SSS II since both debranched amylopectins produce Poisson distributions.