bluuebunny/crossref_metadata_2025 huggingface dataset:
ALGAL FLORA IN THE HULA VALLEY—PAST AND PRESENT
Authors: Pollingher Utsa , Zohary Tamar , Fishbein Tatiana
Published: April 2013

Lake Agmon, a small shallow water body (area 1.1 km2, mean depth <lm) was created in April 1994 as part of the Hula restoration project in the dried peat-soils of the Hula Valley. Until ca. 50 years ago, this area was covered with swamps, extending to the north of Lake Hula. We followed changes over time in the abundance and species composition of the algal populations in Lake Agmon over the initial 4 years that followed its creation, consolidated the existing information on the algal populations of the extinct Lake Hula, and compared the Lake Agmon algal populations with those reported from Lake Hula and with those present in Lake Rinneret. Altogether, 276 algal species were found in Lake Agmon, including 140 chlorophytes, 48 euglenophytes, 34 cyanophytes, 31 diatoms, 8 cryptophytes, 8 dinoflagellates, and 4 chrysophytes. A comprehensive species list for Lake Hula was also compiled, based on the limited published accounts. The similarities between the past and present algal communities in the Hula Valley were great: most diatom, dinoflagellate, chrysophyte, euglenophyte, and large chlorophyte and cyanophyte genera that are seen today in Lake Agmon were also reported from Lake Hula. However, the Hula list of genera was shorter than the Lake Agmon list in some particular categories. The lack of most of the nannoplanktonic Chlorococcales, and all cryptophytes and other small flagellates from the Hula list was attributed to different sampling and preservation methods in the early days; the absence of most filamentous cyanobacteria is considered a real difference, possibly resulting from the more eutrophic status of Lake Agmon. Notably, the dinoflagellatePeridinium gatunense, which blooms annually in Lake Kinneret downstream of the Hula Valley, was not recorded in Lake Hula and did not occur in Lake Agmon.
A COMPARISON OF COMPUTERIZED IMAGE ANALYSIS AND STEREOLOGY AS TOOLS FOR MORPHOLOGICAL STUDY OF ALGAL CELLS
Authors: Fisher Tamar , Berner Tamar , Gal Adiv , Dubinsky Zvy
Published: April 2013

A computerized image analysis package (ImagePro+) was evaluated as an alternative method for morphometric analysis of electron micrographs of microalgal cells. The morphometric analysis was demonstrated with micrographs of the marine alga Nannochloropsis sp. grown under high and low light intensity. We applied the ImagePro+ package to estimate the relative volume of an organelle based on the ratio of perimeters of the organelle and the cell. The measurements included the volumes of chloroplasts, mitochondria, nuclei, vacuoles, and accumulation bodies, all relative to cell volume. The length of thylakoids was measured using the same package.

The results obtained by ImagePro+ were compared to those of the traditional manual and laborious method involving the superimposition of an array of short lines on the micrograph. A high correlation between the methods was found. The following correlations were found for chloroplast, nucleus, and accumulation bodies: 0.96, 0.92, and 0.75, respectively. The correlation between length of thylakoids (ImagePro+) and surface area of thylakoids (superimposition) was 0.82.
SPECIES DIVERSITY GRADIENT TO DARKNESS STRESS IN BLUE-GREEN ALGAE/CYANOBACTERIA: A MICROSCALE TEST IN A PREHISTORIC CAVE, MOUNT CARMEL, ISRAEL
Authors: Vinogradova N. Oxana , Kovalenko Olga V. , Wasser Solomon P. , Nevo Eviatar , Weinstein-Evron Mina
Published: April 2013

Species diversity of epilithic cyanobacteria was studied in a 90 m deep prehistoric el-Wad cave eroded in Cenomanian limestones of Mount Carmel, Israel. The degree of illumination is the most variable index throughout the cave, whereas humidity and temperature vary moderately. In a number of sites inside the cave dripping water occurs due to filtration of rain water. In el-Wad cave 42 species from 20 genera of blue-green algae were found. The share of coccoid forms decreased and filamentous (especially oscillatorial) ones increased from the entrance to the end of the cave. Intensity of light was the governing factor for distribution of cyanobacteria in el-Wad cave; the availability of dripping affected it to a lesser extent due to the constantly high humidity of the air. Diversity of species composition and taxonomic spectrum of cyanophytes was reduced from the entrance to the end of the cave, covarying positively with darkness stress.
A CHECKLIST OF CYANOPHYTA (CYANOBACTERIA) OF ISRAEL AND ADJACENT REGIONS
Authors: Dor Inka
Published: April 2013

Cyanophyta have been investigated in Israel by a number of scientists since early in this century. During the years 1938–1996 fifty-six works were published, describing cyanophyta flora from a variety of aquatic and terrestrial habitats, including Lake Kinneret, Lake Huleh, Mediterranean Sea, Red Sea, Dead Sea, Jordan River, fish ponds, freshwater and polluted reservoirs, rocks and soils, and a number of thermal and freshwater springs. In addition to the 284 taxa described in the published works, the checklist also includes 61 taxa from unpublished materials.
OCCURRENCE OF INTERCELLULAR SPACES IN CAMBIAL RAYS KISHORE S. RAJPUT
Authors: Raiput Kishore S. , Rao K. S.
Published: April 2013

Large intercellular spaces were found in uniseriate as well as multiseriate cambial rays of Tectona grandis L., Azadirachta indica A. Juss., and Tamarindus indica L. During the period when the cambium is inactive, some of the ray cambial cells became oval to circular, resulting in the development of intercellular spaces. However, the cells were polygonal and compactly arranged during active growth of the cambium. Similarly, such spaces were also noticed in the rays of phloem and xylem. The occurrence of intercellular spaces in cambial rays is correlated with the phenology of trees and local climatic factors, and their possible significance is discussed.
EFFECTS OF GRAZING ON EPIPHYTIC LICHEN VEGETATION IN A MEDITERRANEAN MIXED EVERGREEN SCLEROPHYLLOUS AND DECIDUOUS SHRUBLAND (NORTHERN GREECE)
Authors: Pirintsos Stergios Arg , Loppi Stefano , Dalaka Anastasia , De Dominicis Vincenzo
Published: April 2013

The epiphytic lichen vegetation of a heavily grazed Mediterranean mixed evergreen sclerophyllous and deciduous shrubland was studied. Differences in the epiphytic lichen vegetation seem to be largely determined by changes in the architecture of the bushes as well as by the differences in the space between them. In some cases, despite grazing pressure, the epiphytic lichen vegetation does not change dramatically.
SENECIO GLAUCUS L. SUBSP. GLAUCUS, AN EASTERN MEDITERRANEAN TAXON IN THE SANDY SHORES OF SOUTHEASTERN SPAIN
Authors: Alcaraz Francisco , Ríos Segundo , Delgado María José , Inocencio Cristina
Published: April 2013

Senecio glaucus L. subsp. glaucus, a taxon considered native to the Eastern Mediterranean (Israel and Egypt), has been recognized for the first time in littoral sand beaches and dunes of southeastern Spain. A comparative study between Senecio glaucus subsp. glaucus, Senecio glaucus subsp. coronopifolius, and Senecio gallicus was made with herbarium material from Spain and Eastern Mediterranean countries. A line drawing of the Spanish plant and tables of samples of vegetation to show the ecology of this taxon in southeastern Spain are given.
BIODIVERSITY AND INTERSLOPE DIVERGENCE OF VASCULAR PLANTS CAUSED BY MICROCLIMATIC DIFFERENCES AT “EVOLUTION CANYON”, LOWER NAHAL OREN, MOUNT CARMEL, ISRAEL
Authors: Nevo Eviatar , Fragman Ori , Dafni Amots , Beiles Avigdor
Published: April 2013

Species diversity of plants was recorded in 1992 and 1993 at seven stations of the “Evolution Canyon” microsite. Higher solar radiation on the South-Facing Slope (SFS) causes warm, xeric savannoid formation versus temperate, cool, mesic, dense maquis on the North-Facing Slope (NFS), and riverine, segetal plant formations on the Valley Bottom (VB). In an area of 7000 m2, we recorded 320 vascular plant species in 217 genera and 59 families. Plant cover varied from 35% (SFS) to 150% (NFS). Annuals predominated among all life forms (61.3% of all species). SFS and NFS varied in species content, sharing only 31–18% of species. Phytogeographical types varied among the two slopes and valley bottom. Inter-and intraslope species composition varied drastically due to differential microclimatic stresses, thereby demonstrating at a microscale natural selection in action.
MITOCHONDRIAL DNA POLYMORPHISM AND GYNODIOECY IN A NATURAL POPULATION OF ROSMARINUS OFFICINALIS L.
Authors: Hidalgo-Fernández Pablo J. , Pérez-Vicente Rafael , Maldonado M. José , Ubera-Jiménez José L.
Published: April 2013

Mitochondrial genome variability was studied in a gynodioecious population ofRosmarinus officinalisL. Analysis of mitochondrial DNA organization using Southern hybridization with probes for mitochondrial genescoxll, cob.andatp Arevealed a high level of mitochondrial polymorphism; 11 mitotypes were detected in a total of 27 individuals studied. One mitotype was particularly common among male fertile individuals. The remaining mitotypes were found in only one or two individuals, generally male sterile. Polymorphism was thus greater in male sterile than in male fertile individuals. The data presented here suggest that male sterility inRosmarinusis associated with the appearance of mitochondrial genome variants which differ from the standard pattern for male fertile plants.
EFFECTS OF PACLOBUTRAZOL ON THE MORPHOLOGY, STRUCTURE, AND CHLOROPHYLL CONTENT OF REGENERATED PLANTLETS OF MAIZE
Authors: Li Mingjun , Zhang Genfa
Published: April 2013

The morphology, structure, and physiology of regenerated plantlets of maize (Zea mays L.) were affected by paclobutrazol, especially during the hardening process. Hardened plantlets developed dark green leaves and an extensive root system. Plantlets treated with paclobutrazol exhibited retarded development of the stem and leaf, but the lateral growth was improved. After transplanting, survival rate of the plantlets treated with paclobutrazol was up to 3 times that of the controls.
HYBRID STERILITY AS A REPRODUCTIVE BARRIER ISOLATING THE TWO SUBSPECIES OF AEGILOPS GENICOLATA ROTH (GRAMINEAE)
Authors: Ohta Shoji
Published: April 2013

To detect possible reproductive barriers isolating the two subspecies of Aegilops geniculata, ssp. gibberosa was crossed with ssp. geniculata. The two subspecies differ significantly in shape of spikes, spikelet density on spikes, and number of awns on empty glumes. The F hybrids were intermediate in morphology and almost completely sterile. A chromatid bridge with a fragment was observed at first anaphase (AI) of meiosis in some pollen mother cells (PMCs) of the F1 hybrids. Though multivalents were formed at first metaphase (MI) in all the PMCs of the F1 hybrids, the frequency was not higher than that in the intra-subspecific hybrids of ssp. geniculata. These results suggest that the intraspecific sterility is not caused by a gross chromosome differentiation. The hybrid sterility, which is an effective reproductive barrier isolating the two subspecies, might be caused by negative interaction(s) between genes of the two subspecies, or by small chromosomal rearrangements not detectable from chromosome pairing configuration at MI. It is strongly proposed that the delineation of species and infraspecific taxa in the polyploid species of the genus Aegilops is worthy of reassessment from a biosystematic viewpoint.
BIOMASS ALLOCATION AND PHOSPHORUS PRODUCTIVITY OF CAREX SPECIES IN RELATION TO SOIL PHOSPHORUS STATUS
Authors: Pérez-Corona María Esther , Verhoeven Jos T.A.
Published: April 2013

Biomass allocation and P productivity were studied in threeCarexspecies (C. acutiformis, C. diandra, andC. lasiocarpa) that were grown in fen peat soils differing in P content. Biomass allocation to plant parts and P productivity involved significant interactions between soil P status and species.C. acutiformis, a species from highly productive areas, showed higher biomass production, P productivity, leaf area ratio, and specific leaf area under P-deficient conditions thanC. diandraandC. lasiocarpa, both species from less productive areas. Below-ground biomass allocation ofC. acutiformisand above-ground biomass allocation ofC. diandraand C.lasiocarpashowed plasticity in relation to soil P status.

These results were remarkable since C.acutiformis, a species from eutrophic fen areas, was expected to perform worse under P-deficient conditions than those species naturally growing in those areas. Species demands on the chemical composition of the interstitial water, specific abilities to use nondirectly available P pools, faster seed germination, or seedling establishment may contribute to determine the field distribution of fenCarexspecies in relation to soil P status.
THE EVOLUTIONARY ADVANTAGE OF BREEDING FOR TOLERANCE OVER RESISTANCE AGAINST VIRAL PLANT DISEASE
Authors: Salomon Raffi
Published: April 2013

A tolerant strain of a crop permits the propagation of an entire virus population, thus exerting a much lower selection pressure in favor of a virus mutant overcoming resistance. One may suppose that a tolerant crop may build up a large virus reservoir and therefore increase the chance of emergence of a more virulent type. However, the tolerant crop exerts a much lower selective pressure for a given virus line, and therefore the new virulent type remains a very low proportion of the total virus population. Susceptible crops, into which resistance to a given virus was bred, may be immune to this virus infection, thus preventing the buildup of a large virus reservoir. However, other host crops around it, or wild weeds facilitate propagation of this virus. This peripheral buildup of virus reservoir in the vicinity of the resistant crop creates a strong selection pressure for the propagation of the mutants overcoming resistance. Therefore, the planting of monoculture of a resistant crop accelerates the emergence of virulent virus lines that overcome this resistance. There is no reason to assume that resistance introduced into transgenic plants will be different. In the long run, tolerant crops may have the advantage over resistant crops, preserving for a longer time conditions in which virus infection causes only minimal damage. The production of tolerance to virus infection is an approach not yet favored by breeders and seed producers. However, it may be regarded as a less expensive, additional route to reduce the damage to crops inflicted by viral diseases.
LIGHT-STIMULATED LEAF GROWTH ON INTACT AND EXCISED BEAN PLANTS (PHASEOLUS VULGARIS L.). I. CHARACTERIZATION OF BASIC RESPONSES
Authors: Lavee Shimon , Van Volkenburgh Elizabeth , Cleland Robert E.
Published: April 2013

The effect of root excision on the growth of primary leaves, petioles, and epicotyls of bean plants (Phaseolus vulgaris L.) has been investigated for plants growing in various light conditions. Plants were initially grown in either continuous dim red light (RL; 4 μmol m−2S−1) or bright white light (WL; 100 μmol; m−2S−1, 16 h light: 8 h dark photoperiod) for 10 days. On day 10, some plants were excised. Then, both intact and excised plants were returned to RL or WL, or switched to the other light treatment (RL to WL, WL to RL). Exposure to WL on day 10 promoted leaf expansion and inhibited petiole and epicotyl growth, regardless of light pretreatments before day 10. Root excision reduced leaf expansion by 40–50% both in WL and RL. Petiole and epicotyl growth were less affected. Removal of the cotyledons or the stem apex caused a slight but significant reduction of leaf elongation in both intact and excised plants. Apex removal reduced epicotyl elongation but did not stop it. Although excision of roots partially inhibited leaf and epicotyl development, the relative response of excised plants to the light treatments was similar to that of intact plants. These results justify the use of derooted plants to study leaf growth in a “whole plant” excised system.
EFFECT OF SLOPE ASPECT ON SOIL AND VEGETATION PROPERTIES ALONG AN ARIDITY TRANSECT
Authors: Kutiel Pua , Lavee Hanoch
Published: April 2013

This study has investigated the effect of south- and north-facing hillslopes (SFS and NFS, respectively) on soil and vegetation properties along a climatic transect that covers four climatic zones: Mediterranean, semiarid, arid, and extreme-arid. The results indicate that differences between NFS and SFS in organic matter and soil moisture contents were significantly higher in the Mediterranean zone than in any other site along the climatic transect, particularly at the end of the rainy season. Both soil properties were higher on NFS than on SFS. Similarly, differences between the opposite hillslopes in species richness along the climatic transect were found significant only in the Mediterranean zone, where species richness was higher on the SFS than on the NFS. However, species diversity on SFS was significantly higher than that on NFS at all sites, except for the semiarid zone, where no significant difference between aspects was found. Species diversity on SFS changed along the climatic transect at an almost linear rate, while on NFS there was a sharp increase from the extreme-arid zone to the semiarid zone, followed by a decline moving towards the Mediterranean zone. Vegetation cover along the climatic transect was higher on NFS than on SFS, except for the extreme-arid zone, where no significant difference was found. The general conclusions are: (a) The most significant differences in soil and vegetation properties between NFS and SFS are found in the Mediterranean zone, mainly at the end of the rainy season; in the semiarid, arid, and extreme-arid zones the differences are small and generally negligible, (b) The spatial and seasonal differences on SFS are smaller than those on NFS.
SANDSTONE OUTCROPS—A MAJOR REFUGIUM OF MEDITERRANEAN FLORA IN THE XERIC PART OF JORDAN
Authors: Danin Avinoam
Published: April 2013

Plants growing in sandstone outcrops at the western escarpments of the Jordanian plateau, in the Tafila-Petra-Ras en Naqb area, represent a unique refugium for Mediterranean flora in an area receiving 100–300 mm of rainfall annually, located at the transition between desert and shrub-steppe vegetation of southwestern Jordan. The occurrence of large outcrops of smooth-faced hard sandstone and limestone cliffs at elevations from sea level to 1,200 m above sea level enabled the long persistence of various kinds of habitats that supported hundreds of Mediterranean relict plant species of all growth forms that survived from periods when the climate was moister. The continuity, in SW Jordan, of the refugium habitat enabled a rich Mediterranean flora to survive in the desert including many endemic species. The Jordanian refugia are much richer floristically than those of the Israeli and Sinai deserts.
MORPHOLOGICAL AND ANATOMICAL STRUCTURE OF GALLS IN GENISTA FLORIDA L. SUBSP. POLYGALIPHYLLA (BROT.) COUTHINO (LEGUMINOSAE)
Authors: Estrelles Elena , Iranzo Julio , Martínez-Solís Isabel , Ibars M. Anna
Published: April 2013

This paper describes the morphology and anatomy of a structure which appears in the floral racemes of Genista florida L. subsp. polygaliphylla (Brot.) Couthino. In this subspecies the floral racemes have a small number of flowers. This structure develops quite frequently in this taxon, which is found in the northwest of the Iberian Peninsula, but never in Genista florida subsp. florida. Its morphology is simple: bottle-shaped, wide at the base and elongated to a narrow peak at the upper extreme. Anatomical examination shows that these structures have a close similarity to flowers. Since they develop by the oviposition of one insect of the Cecidomyiidae family in the floral buds, they can be considered galls. This fact is of great interest in the taxonomy of the group because the number of flowers is a differential character between the two subspecies of G. florida.
QUERCUS ICHNUSAE (FAGACEAE), A NEW SPECIES FROM SARDINIA
Authors: Mossa Luigi , Bacchetta Gianluigi , Brullo Salvatore
Published: April 2013

A new species of Quercus, Q. ichnusae, endemic to Sardinia is described and illustrated. Its distribution and relationships with the other deciduous oaks occurring on the island are examined.
LIGHT REGULATION OF ANTHOCYANIN ACCUMULATION AND CHALCONE SYNTHASE GENE EXPRESSION IN PETUNIA FLOWERS
Authors: Katz Anat , Weiss David
Published: April 2013

We have previously shown that light is essential for anthocyanin synthesis in detached petunia flowers. In this study, we examined the effect of light quality on anthocyanin accumulation and on the expression of the anthocyanin biosynthetic gene chalcone synthase (chs) in the attached petunia flowers. When plants were kept for 48 h in the dark,chsexpression could not be detected. Blue light and red light promoted the expression of the gene to similar levels, whereas the effect of green light was slightly smaller. Neither UV-A nor UV-B radiation were required for anthocyanin accumulation, or for the induction and maintenance ofchsexpression. The results of this study show that light is essential for anthocyanin synthesis in petunia flowers and that its active spectrum includes most of the visible part but not UV radiation.
LIGHT-STIMULATED LEAF GROWTH ON INTACT AND EXCISED BEAN PLANTS (PHASEOLUS VULGARIS L.) III. EFFECT OF LIGHT INTENSITY
Authors: Lavee Shimon , Van Volkenburgh Elizabeth , Cleland E. Robert
Published: April 2013

The effect of light intensity on primary bean leaf unfolding and elongation was studied with intact and excised 10-day-old plants grown under red light. Continuous light of 40 μmol; m−2S−1 was enough to induce maximal leaf expansion both on intact and excised bean plants. Lower light intensities had a partial effect. The growth rate during the first 24 h in light was linearly related to light intensity up to 130 μmol; m−2S−1, although this light intensity was already supra-optimal for final leaf size. The minimal amount of light energy needed for full leaf expansion was about 15 mol photons m−2. The mode of light application, level of intensity, and irradiance duration were not critical when the total energy requirement was fulfilled. Under insufficient light applications for full leaf expansion, interrupted irradiance and longer low light intensity application induced leaf elongation more efficiently. Generally, the effect of different white light intensities on primary bean leaf expansion was the same on both intact and excised red-light-grown plants.
PLASMODESMAL MODIFICATIONS AND DISTRIBUTION OF TOSPO VIRUS IN POTATO AND TOMATO
Authors: Garg Ishwar D. , Paul Khurana S.M.
Published: April 2013

The tospovirus isolate on tomato was found to be systemic while the one on potato was non-systemic. The virus was present in all the tissues except xylem vessels in tomato, while it was often found only in the cortical cells of potato stems. Virions were detected in all cells of phloem tissue in tomato, while none were present in the case of potato. Plasmodesmata were present between phloem parenchyma and the phloem sieve tubes in infected tomato but none were present in infected potato. There were pronounced plasmodesmal changes in response to infection in tomato. These included dissolution of the desmotubule (central rod-like structure), making the plasmodesmata pore-like structures with a diameter of ca. 45 nm, which contained electron-dense material, presumably ribonucleoprotein of the virus. No such changes were found in infected potato. These results of comparative studies suggested that the virus was non-systemic in potato due to its non-loading into the phloem and consequently lacked long distance transport.
MORPHOLOGY, DISTRIBUTION, AND HISTOCHEMISTRY OF SECRETORY STRUCTURES IN VEGETATIVE ORGANS OF SANTOLINA LEUCANTHA BERTOL. (ASTERACEAE)
Authors: Pagni Anna Marta , Masini Antonio
Published: April 2013

In the vegetative organs of Santolina leucantha Bertol. (Anthemideae), two distinct types of secretory structures are present: Internal secretory ducts and external glandular trichomes. The ducts are variable in morphology and location, depending on the organ in which they are present. The trichomes, however, show the same structure everywhere. In the roots, there are also scattered cells rich in secretion that are distributed in the periphery of the cortical cylinder. The histochemical analysis of the secretion reveals the presence in all the vegetative organs of many important secondary compounds. Vegetative secretory structures are similar to those in the capitulum we have described in a previous paper.
A Summary of Meeting Proceedings on Addressing Variability around the Cut Point in Serial Interferon-γ Release Assay Testing
Authors: Daley Charles L. , Reves Randall R. , Beard Melodie A. , Boyle Jeffrey , Clark Richard B. , Beebe James L. , Catanzaro Antonino , Chen Lisa , Desmond Edward , Dorman Susan E. , Hudson T. Warner , Lardizabal Alfred A. , Kapoor Hema , Marder David C. , Miranda Cyndee , Narita Masahiro , Reichman Lee , Schwab Dale , Seaworth Barbara J. , Terpeluk Paul , Thanassi Wendy , Kawamura L. Masae
Published: April 2013

On June 13, 2012, a group of key stakeholders, leaders, and national experts on tuberculosis (TB), occupational health, and laboratory science met in Atlanta, Georgia, to focus national discussion on the higher than expected positive results occurring among low-risk, unexposed healthcare workers undergoing serial testing with interferon-γ release assays (IGRAs). The objectives of the meeting were to present the latest clinical and operational research findings on the topic, to discuss evaluation and treatment algorithms that are emerging in the absence of national guidance, and to develop a consensus on the action steps needed to assist programs and physicians in the interpretation of serial testing IGRA results. This report summarizes its proceedings.
An HMM-based algorithm for evaluating rates of receptor–ligand binding kinetics from thermal fluctuation data
Authors: Ju Lining , Wang Yijie Dylan , Hung Ying , Wu Chien-Fu Jeff , Zhu Cheng
Published: April 2013

Motivation: Abrupt reduction/resumption of thermal fluctuations of a force probe has been used to identify association/dissociation events of protein–ligand bonds. We show that off-rate of molecular dissociation can be estimated by the analysis of the bond lifetime, while the on-rate of molecular association can be estimated by the analysis of the waiting time between two neighboring bond events. However, the analysis relies heavily on subjective judgments and is time-consuming. To automate the process of mapping out bond events from thermal fluctuation data, we develop a hidden Markov model (HMM)-based method.

Results: The HMM method represents the bond state by a hidden variable with two values: bound and unbound. The bond association/dissociation is visualized and pinpointed. We apply the method to analyze a key receptor–ligand interaction in the early stage of hemostasis and thrombosis: the von Willebrand factor (VWF) binding to platelet glycoprotein Ibα (GPIbα). The numbers of bond lifetime and waiting time events estimated by the HMM are much more than those estimated by a descriptive statistical method from the same set of raw data. The kinetic parameters estimated by the HMM are in excellent agreement with those by a descriptive statistical analysis, but have much smaller errors for both wild-type and two mutant VWF-A1 domains. Thus, the computerized analysis allows us to speed up the analysis and improve the quality of estimates of receptor–ligand binding kinetics.

Contact:  jeffwu@isye.gatech.edu or cheng.zhu@bme.gatech.edu
Density distributions of outflow-driven turbulence
Authors: Moraghan Anthony , Kim Jongsoo , Yoon Suk-Jin
Published: April 2013

Protostellar jets and outflows are signatures of star formation and promising mechanisms for driving supersonic turbulence in molecular clouds. We quantify outflow-driven turbulence through three-dimensional numerical simulations using an isothermal version of the robust total variation diminishing code. We drive turbulence in real space using a simplified spherical outflow model, analyse the data through density probability distribution functions (PDFs), and investigate the core formation rate per free-fall time (CFRff). The real-space turbulence-driving method produces a negatively skewed density PDF possessing an enhanced tail on the low-density side. It deviates from the log-normal distributions typically obtained from Fourier-space turbulence driving at low densities, but can provide a good fit at high densities, particularly in terms of mass-weighted rather than volume-weighted density PDF. Due to this fact, we suggest that the CFRff determined from a Fourier-driven turbulence model could be comparable to that of our particular real-space-driving model, which has a ratio of solenoidal to compressional components from the resulting turbulence velocity fields of ∼0.6.
Extrahepatic Cholangiocyte Cilia Are Abnormal in Biliary Atresia
Authors: Karjoo Sara , Hand Nicholas J. , Loarca Lorena , Russo Pierre A. , Friedman Joshua R. , Wells Rebecca G.
Published: April 2013

Objectives:

Biliary atresia (BA) is a rapidly progressive form of biliary fibrosis affecting neonates. We previously reported that primary cilia on the intrahepatic cholangiocytes of patients with both syndromic and nonsyndromic BA were structurally abnormal. Our objective was to determine whether extrahepatic cholangiocytes in human biliary atesia, intrahepatic and extrahepatic cholangiocytes of rhesus rotavirus (RRV)‐infected neonatal mice, and RRV‐infected primary neonatal extrahepatic cholangiocytes also demonstrate ciliary abnormalities.

Methods:

The livers of neonatal BALB/c mice injected with RRV that developed jaundice, human extrahepatic bile duct samples obtained at time of hepatoportoenterostomy, and RRV‐infected primary neonatal cholangiocytes were stained with antibodies against acetylated α tubulin to identify primary cilia.

Results:

Extrahepatic cholangiocytes from RRV‐treated mice demonstrated minimal loss of primary cilia at day 3 but almost complete loss at day 8 and partial loss at day 12. No changes were seen in mouse intrahepatic bile ducts at any of the time points. In the human BA samples, primary cilia were almost completely absent from extrahepatic duct cholangiocytes. There were, however, abundant cilia in the peribiliary glands adjacent to extrahepatic ducts in the BA sample. Cilia in RRV‐infected primary neonatal cholangiocytes were significantly decreased compared with controls.

Conclusions:

Primary cilia are selectively lost from neonatal extrahepatic but not intrahepatic cholangiocytes after RRV infection in BALB/c mice. The cilia are also decreased in RRV‐infected primary cholangiocytes and the extrahepatic ducts from human patients with BA. This suggests that ciliary abnormalities are part of the pathophysiology of BA.
Advances in molecular surveillance of Clostridium difficile in Bulgaria
Authors: Dobreva Elina G. , Ivanov Ivan N. , Vathcheva-Dobrevska Rossitza S. , Ivanova Katucha I. , Asseva Galina D. , Petrov Petar K. , Kantardjiev Todor V.
Published: April 2013

The increasing incidence of Clostridium difficile infection (CDI) in Bulgaria has indicated the need to implement better surveillance approaches. The aim of the present work was to improve the current surveillance of CDI in Bulgaria by introducing innovative methods for identification and typing. One hundred and twenty stool samples obtained from 108 patients were studied over 4 years from which 32 C. difficile isolates were obtained. An innovative duplex EvaGreen real-time PCR assay based on simultaneous detection of the gluD and tcdB genes was developed for rapid C. difficile identification. Four toxigenic profiles were distinguished by PCR: A+B+CDT− (53.1 %, 17/32), A−B+CDT− (28.1 %, 9/32), A+B+CDT+ (9.4 %, 3/32) and A−B−CDT− (9.4 %, 3/32). PCR ribotyping and multilocus variable number of tandem repeat analysis (MLVA7) were used for molecular characterization of the isolates. In total, nine distinct ribotypes were confirmed and the most prevalent for Bulgarian hospitals was 017 followed by 014/020, together accounting for 44 % of all isolates. Eighteen per cent of the isolates (6/32) did not match any of the 25 reference ribotypes available in this study. Twenty-four MLVA7 genotypes were detected among the clinical C. difficile isolates, distributed as follows: five for 017 ribotype, two for 014/020, 001, 002, 012 and 046 each, and one each for ribotypes 023, 070 and 078. The correlation between the typing methods was significant and allowed the identification of several clonal complexes. These results suggest that most C. difficile cases in the eight Bulgarian hospitals studied were associated with isolates belonging to the outbreak ribotypes 017 and 014/20, which are widely distributed in Europe. The real-time PCR protocol for simultaneous detection of gluD and tcdB proved to be very effective and improved C. difficile identification and confirmation of clinical C. difficile isolates.
A RANKL–PKCβ–TFEB signaling cascade is necessary for lysosomal biogenesis in osteoclasts
Authors: Ferron Mathieu , Settembre Carmine , Shimazu Junko , Lacombe Julie , Kato Shigeaki , Rawlings David J. , Ballabio Andrea , Karsenty Gerard
Published: April 2013

Bone resorption by osteoclasts requires a large number of lysosomes that release proteases in the resorption lacuna. Whether lysosomal biogenesis is a consequence of the action of transcriptional regulators of osteoclast differentiation or is under the control of a different and specific transcriptional pathway remains unknown. We show here, through cell-based assays and cell-specific gene deletion experiments in mice, that the osteoclast differentiation factor RANKL promotes lysosomal biogenesis once osteoclasts are differentiated through the selective activation of TFEB, a member of the MITF/TFE family of transcription factors. This occurs following PKCβ phosphorylation of TFEB on three serine residues located in its last 15 amino acids. This post-translational modification stabilizes and increases the activity of this transcription factor. Supporting these biochemical observations, mice lacking in osteoclasts—either TFEB or PKCβ—show decreased lysosomal gene expression and increased bone mass. Altogether, these results uncover a RANKL-dependent signaling pathway taking place in differentiated osteoclasts and culminating in the activation of TFEB to enhance lysosomal biogenesis—a necessary step for proper bone resorption.
Respiration control of multicellularity in Bacillus subtilis by a complex of the cytochrome chain with a membrane-embedded histidine kinase
Authors: Kolodkin-Gal Ilana , Elsholz Alexander K.W. , Muth Christine , Girguis Peter R. , Kolter Roberto , Losick Richard
Published: April 2013

Bacillussubtilis forms organized multicellular communities known as biofilms wherein the individual cells are held together by a self-produced extracellular matrix. The environmental signals that promote matrix synthesis remain largely unknown. We discovered that one such signal is impaired respiration. Specifically, high oxygen levels suppressed synthesis of the extracellular matrix. In contrast, low oxygen levels, in the absence of an alternative electron acceptor, led to increased matrix production. The response to impaired respiration was blocked in a mutant lacking cytochromes caa3 and bc and markedly reduced in a mutant lacking kinase KinB. Mass spectrometry of proteins associated with KinB showed that the kinase was in a complex with multiple components of the aerobic respiratory chain. We propose that KinB is activated via a redox switch involving interaction of its second transmembrane segment with one or more cytochromes under conditions of reduced electron transport. In addition, a second kinase (KinA) contributes to the response to impaired respiration. Evidence suggests that KinA is activated by a decrease in the nicotinamide adenine dinucleotide (NAD+)/NADH ratio via binding of NAD+ to the kinase in a PAS domain A-dependent manner. Thus, B. subtilis switches from a unicellular to a multicellular state by two pathways that independently respond to conditions of impaired respiration.
Mobile element scanning (ME-Scan) identifies thousands of novel Alu insertions in diverse human populations
Authors: Witherspoon David J. , Zhang Yuhua , Xing Jinchuan , Watkins W. Scott , Ha Hongseok , Batzer Mark A. , Jorde Lynn B.
Published: April 2013

Alu retrotransposons are the most numerous and active mobile elements in humans, causing genetic disease and creating genomic diversity. Mobile element scanning (ME-Scan) enables comprehensive and affordable identification of mobile element insertions (MEI) using targeted high-throughput sequencing of multiplexed MEI junction libraries. In a single experiment, ME-Scan identifies nearly all AluYb8 and AluYb9 elements, with high sensitivity for both rare and common insertions, in 169 individuals of diverse ancestry. ME-Scan detects heterozygous insertions in single individuals with 91% sensitivity. Insertion presence or absence states determined by ME-Scan are 95% concordant with those determined by locus-specific PCR assays. By sampling diverse populations from Africa, South Asia, and Europe, we are able to identify 5799 Alu insertions, including 2524 novel ones, some of which occur in exons. Sub-Saharan populations and a Pygmy group in particular carry numerous intermediate-frequency Alu insertions that are absent in non-African groups. There is a significant dearth of exon-interrupting insertions among common Alu polymorphisms, but the density of singleton Alu insertions is constant across exonic and nonexonic regions. In one case, a validated novel singleton Alu interrupts a protein-coding exon of FAM187B. This implies that exonic Alu insertions are generally deleterious and thus eliminated by natural selection, but not so quickly that they cannot be observed as extremely rare variants.
Weak limits and their calculation in analog signal theory
Authors: Jurić Željko , Šiljak Harun
Published: April 2013

Purpose

This paper aims to improve the mathematical justification of certain analog signal theory concepts and offer a rigorous framework for it.

Design/methodology/approach

The framework relies on functional analysis, namely theory of distributions and the concept of weak limit. Its notation is adjusted to resemble the notation usually used in engineering signal theory. It can be used to prove in a rigorous manner already established results in signal theory, but also to establish new ones.

Findings

Examples have shown the lack of rigour caused by using ordinary calculus in proving fundamental signal theoretic results. On that basis, concepts of limit, Fourier transform and derivative are revisited in the spirit of functional analysis. A new useful formula for weak limit computation is proved.

Originality/value

Functional analysis is efficiently used in signal theory in a manner approachable by engineers. An original and efficient formula for weak limit computation is presented and proved.
Longitudinal profiles of expressive vocabulary, syntax and pragmatic language in boys with fragile X syndrome or Down syndrome
Authors: Martin Gary E. , Losh Molly , Estigarribia Bruno , Sideris John , Roberts Joanne
Published: April 2013

Background

Fragile X syndrome (FXS) and Down syndrome (DS) are the two leading genetic causes of intellectual disability, and FXS is the most common known genetic condition associated with autism. Both FXS and DS are associated with significant language impairment, but little is known about expressive language across domains over time or the role of autism in language development in FXS.

Aims

To compare three domains of language production (vocabulary, syntax, pragmatics) over time within and across groups of boys with FXS with and without autism spectrum disorder (FXS‐ASD, FXS‐O), boys with DS, and typically developing (TD) boys.

Methods & Procedures

Twenty‐nine boys with FXS‐O, 40 boys with FXS‐ASD, 34 boys with DS, and 48 younger TD boys of similar non‐verbal mental age living in the United States participated in the study. The Antonyms, Syntax Construction and Pragmatic Judgment subtests of the Comprehensive Assessment of Spoken Language were administered annually over 3 years.

Outcomes & Results

TD boys scored higher than all other groups on all three subtests; boys with FXS‐O and FXS‐ASD scored higher than boys with DS in Syntax Construction; and boys with FXS‐O scored higher than boys with FXS‐ASD in Pragmatic Judgment. Within‐group patterns varied between groups. Overall, the TD group showed significantly more change over time than all other groups.

Conclusions & Implications

Findings suggest that expressive language skills and growth across various domains are more impaired in boys with FXS and DS than would be expected based on non‐verbal mental age, that for boys with DS syntax is more impaired than would be expected based on intellectual disability, and that autism status affects pragmatic language in boys with FXS. Findings suggest that language production across domains should be addressed during assessment and intervention for boys with FXS and boys with DS, with differing group profiles also suggesting potentially different areas of focus.
The Personal Agreement System of Zbu Rgyalrong (Ngyaltsu Variety)
Authors: Gong Xun
Published: April 2013

In this paper, the personal agreement system of the Ngyaltsu variety of Zbu rGyalrong is described, the first such description for this rarely documented Sino‐Tibetan language. The agreement pattern is characterised by a direct‐inverse system, analysed in detail using the conceptual apparatus from. The system is then compared with those of three neighbouring rGyalrong languages: Eastern rGyalrong, Japhug and Tshobdun, where it is suggested, especially from the behaviour of closed‐syllable stems in Eastern rGyalrong, that the person suffixes across rGyalrong are internally structured, the 1sg suffix having a particularly close relationship with the stem.
The effect of incorporating calcium lactate in the saline solution on improving the shelf life of Fiordilatte cheese
Authors: Michele Faccia , Luisa Angiolillo , Marianna Mastromatteo , Amalia Conte , Matteo Alessandro Del Nobile
Published: April 2013

The effect of calcium lactate (CL) on both the sensory and microbiological quality of Fiordilatte cheese was evaluated. The novelty of this work is the addition of the salt to the product brine, prior to packaging, instead of adding calcium during process. Cheese quality was monitored for 8 days by evaluating the spoilage and the development of the main sensory attributes. Results demonstrated a modest inhibition effect of CL on the microbial proliferation, whereas from a sensory point of view, a somewhat improvement in the odour and texture was recorded, thus suggesting CL as a valid alternative to calcium chloride.
The physicochemical properties of yoghurt supplemented with microencapsulated peanut sprout extract, a possible functional ingredient
Authors: Lee Yun‐Kyung , Al Mijan Mohammad , Ganesan Palanivel , Yoo Sanghun , Kwak Hae‐Soo
Published: April 2013

This study was designed to determine the physicochemical and sensory properties of yoghurt supplemented with powdered peanut sprout extract microcapsules (PPSEM) (3–10 μm) during storage at 4 °C for 16 days. The releasing rates of the polyphenol, resveratrol, from yoghurts were minimised at lower concentrations of PPSEM (0.25 and 0.5%, w/v). The viscosity decreased gradually with higher concentrations of PPSEM added. In the sensory test, there were significant increases in yellowness, peanut and cooked scores (P < 0.05). Based on the results, it is concluded that the low concentrations (0.25 and 0.50%, w/v) could be used to produce PPSEM‐supplemented yoghurt without significant adverse effects on the physicochemical and functional properties.
Comparison of buffalo cottage cheese made from aqueous extract of Withania coagulans with commercial calf rennet
Authors: Khan Rao Sanaullah , Masud Tariq
Published: April 2013

An aqueous extract of Withania coagulans was used to prepare cottage cheese from buffalo milk and its quality attributes were compared with cheese made from commercial rennet. Both cheeses contain satisfactory ranges of 49.6–54.7% moisture, 21.3–24.3% fat and 21.4–23.6% protein. The type of coagulant had no significant effect on acidity, protein and ash contents of both the cheeses. W. coagulans cheese showed a significantly (P < 0.05%) higher pH and moisture contents. Similarly, no marked differences were observed in their organoleptic evaluation, actual and theoretical yield. These results supported the fact that W. coagulans is a promising rennet substitute for cottage cheesemaking.
Dietary intakes of zinc and copper and cardiovascular risk factors in Tehranian adults: Tehran Lipid and Glucose Study
Authors: Shab‐Bidar Sakineh , Hosseini‐Esfahani Firoozeh , Mirmiran Parvin , Mehran Mahya , Azizi Fereidoun
Published: April 2013

Aim

The aim of the present study was to investigate the intakes of zinc and copper in relation to cardiovascular disease (CVD) risk factors in a group of Tehranian adults.

Methods

The present cross‐sectional study was conducted on 2750 individuals, selected among participants of the Tehran Lipid and Glucose Study. Dietary intake was assessed using a validated semi‐quantitative food frequency questionnaire. Metabolic syndrome (MetS) and CVD risk factors were evaluated.

Results

After adjustment of possible confounders, the dietary zinc intake was found to have a negative relation with serum HDL‐C (β = −0.47, P = 0.027), triglycerides (TG) (β = −0.003, P = 0.032) and 2‐hour blood glucose (β = −1.6, P = 0.017) levels in women. Prevalence of MetS was not associated with dietary zinc intake when confounding factors were included in the statistical model. Comparing the highest versus the lowest intake categories of dietary copper, the multivariable adjusted odds ratios for HDL‐C, fasting blood glucose(FBG), TG and MetS were 1.75 (1.43–2.25)(P for trend = 0.003), 0.90 (0.76–1.23)(P for trend = 0.017), 0.11(0.08–0.21) (P for trend = 0.042) and 0.19 (0.15–0.38)(P for trend = 0.023), respectively.

Conclusions

The results indicate gender differences in the association between zinc intake and CVD risk factors; in women, lower consumption of dietary zinc was associated with increased levels of serum TG and 2‐hour BG and decreased levels of HDL‐C, while Copper intake was negatively associated with higher risk of MetS and its components (FBG, HDL‐C and TG).