Cracks in the palisade cuticle of soybean seed coats correlate with their permeability to water

BACKGROUND AND AIMS: Soybean (Glycine max) is among the many legumes that are well known for 'hardseededness'. This feature can be beneficial for long-term seed survival, but is undesirable for the food processing industry. There is substantial disagreement concerning the mechanisms and related structures that control the permeability properties of soybean seed coats. In this work, the structural component that controls water entry into the seed is identified. METHODS: Six soybean cultivars were tested for their seed coat permeabilities to water. To identify the structural feature(s) that may contribute to the determination of these permeabilities, fluorescent tracer dyes, and light and electron microscopic techniques were used. KEY RESULTS: The cultivar 'Tachanagaha' has the most permeable seed coat, 'OX 951' the least permeable seed coat, and the permeabilities of the rest ('Harovinton', 'Williams', 'Clark L 67-3469', and 'Harosoy 63') are intermediate. All seeds have surface deposits, depressions, a light line, and a cuticle about 0.2 microm thick overlaying the palisade layer. In permeable cultivars the cuticle tends to break, whereas in impermeable seeds of 'OX 951' it remains intact. In the case of permeable seed coats, the majority of the cracks are from 1 to 5 micro m wide and from 20 to 200 micro m long, and occur more frequently on the dorsal side than in other regions of the seed coat, a position that correlates with the site of initial water uptake. CONCLUSIONS: The cuticle of the palisade layer is the key factor that determines the permeability property of a soybean seed coat. The cuticle of a permeable seed coat is mechanically weak and develops small cracks through which water can pass. The cuticle of an impermeable seed coat is mechanically strong and does not crack under normal circumstances.     

Comparative water-use efficiency of Sporobolus arabicus and Leptochloa fusca and its relation with carbon-isotope discrimination under semi-arid conditions

Water-use efficiency (WUE) of Leptochloa fusca (L.) Kunth (Kallar grass) and Sporobolus arabicus Boiss. was determined under different soil moisture regimes. Plants grown in lysimeters were subjected to three soil moisture regimes, viz. well-watered (100%), medium-watered (75%), and low-watered (50%) of total available water (TAW). The soil moisture was restored on alternate days by adding the required volume of water on the basis of neutron moisture meter readings taken from neutron access tubes installed in each lysimeter. The grasses were harvested after suitable intervals (4 months) to obtain maximum biomass. Leaf samples collected at each harvest were analyzed for carbon-isotope discrimination (¹³C) with an isotope ratio (¹³C/¹²C) mass spectrometer. Results indicated significant differences in WUE of both grasses subjected to different water regimes. Sporobolus arabicus showed higher WUE than Kallar grass. However, Kallar grass showed better value of yield response factor (k _y = 0.649) compared with Sporobolus (k _y = 1.06) over the entire season. The data confirm that these grasses can be grown successfully in water-limited environments by selecting an optimum soil moisture level for maximum biomass production. The mean carbon-isotope discrimination (¹³C) of Kallar grass (–14.4) and Sporobolus (–12.8) confirm that both are C₄ plants. The carbon-isotope discrimination () was significantly and negatively correlated with WUE of the two species studied. The results of the present study confirm that ¹³C or of leaves can be used as good predictor of WUE in some C₄ plants.     

The database for aggregate analysis of ClinicalTrials.gov (AACT) and subsequent regrouping by clinical specialty

BACKGROUND: The ClinicalTrials.gov registry provides information regarding characteristics of past, current, and planned clinical studies to patients, clinicians, and researchers; in addition, registry data are available for bulk download. However, issues related to data structure, nomenclature, and changes in data collection over time present challenges to the aggregate analysis and interpretation of these data in general and to the analysis of trials according to clinical specialty in particular. Improving usability of these data could enhance the utility of ClinicalTrials.gov as a research resource. METHODS/PRINCIPAL RESULTS: The purpose of our project was twofold. First, we sought to extend the usability of ClinicalTrials.gov for research purposes by developing a database for aggregate analysis of ClinicalTrials.gov (AACT) that contains data from the 96,346 clinical trials registered as of September 27, 2010. Second, we developed and validated a methodology for annotating studies by clinical specialty, using a custom taxonomy employing Medical Subject Heading (MeSH) terms applied by an NLM algorithm, as well as MeSH terms and other disease condition terms provided by study sponsors. Clinical specialists reviewed and annotated MeSH and non-MeSH disease condition terms, and an algorithm was created to classify studies into clinical specialties based on both MeSH and non-MeSH annotations. False positives and false negatives were evaluated by comparing algorithmic classification with manual classification for three specialties. CONCLUSIONS/SIGNIFICANCE: The resulting AACT database features study design attributes parsed into discrete fields, integrated metadata, and an integrated MeSH thesaurus, and is available for download as Oracle extracts (.dmp file and text format). This publicly-accessible dataset will facilitate analysis of studies and permit detailed characterization and analysis of the U.S. clinical trials enterprise as a whole. In addition, the methodology we present for creating specialty datasets may facilitate other efforts to analyze studies by specialty groups.     

Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses

We previously identified a group of atypical mobile elements designated Mavericks from the nematodes Caenorhabditis elegans and C. briggsae and the zebrafish Danio rerio. Here we present the results of comprehensive database searches of the genome sequences available, which reveal that Mavericks are widespread in invertebrates and non-mammalian vertebrates but show a patchy distribution in non-animal species, being present in the fungi Glomus intraradices and Phakopsora pachyrhizi and in several single-celled eukaryotes such as the ciliate Tetrahymena thermophila, the stramenopile Phytophthora infestans and the trichomonad Trichomonas vaginalis, but not detectable in plants. This distribution, together with comparative and phylogenetic analyses of Maverick-encoded proteins, is suggestive of an ancient origin of these elements in eukaryotes followed by lineage-specific losses and/or recurrent episodes of horizontal transmission. In addition, we report that Maverick elements have amplified recently to high copy numbers in T. vaginalis where they now occupy as much as 30% of the genome. Sequence analysis confirms that most Mavericks encode a retroviral-like integrase, but lack other open reading frames typically found in retroelements. Nevertheless, the length and conservation of the target site duplication created upon Maverick insertion (5- or 6-bp) is consistent with a role of the integrase-like protein in the integration of a double-stranded DNA transposition intermediate. Mavericks also display long terminal-inverted repeats but do not contain ORFs similar to proteins encoded by DNA transposons. Instead, Mavericks encode a conserved set of 5 to 9 genes (in addition to the integrase) that are predicted to encode proteins with homology to replication and packaging proteins of some bacteriophages and diverse eukaryotic double-stranded DNA viruses, including a DNA polymerase B homolog and putative capsid proteins. Based on these and other structural similarities, we speculate that Mavericks represent an evolutionary missing link between seemingly disparate invasive DNA elements that include bacteriophages, adenoviruses and eukaryotic linear plasmids.     

Interaction Between Essential Elements Selenium and Zinc with Cadmium and Mercury in Samples from Hypertensive Patients

The abnormal metabolism of metal ions plays an important role in health and disease conditions; hence, the studies about them have received much interest. The objective of this study was to evaluate the association between trace and toxic elements zinc (Zn), cadmium (Cd), selenium (Se), and mercury (Hg) in biological samples (scalp hair, blood, and urine) of hypertensive patients (n?=?257), residents of Hyderabad, Pakistan. For comparison purpose, the biological samples of age-matched healthy controls were selected as referents. The concentrations of trace and toxic elements were measured by atomic absorption spectrophotometer prior to microwave-assisted acid digestion. The validity and accuracy of the methodology was checked using certified reference materials and by the conventional wet acid digestion method. The recovery of all studied elements was found in the range of 96.4–99.1 % in certified reference materials. The results of this study showed that the mean values of Cd and Hg were significantly higher in scalp hair, blood, and urine samples of hypertensive patients than in referents (P?<?0.001), whilst the concentrations of Zn and Se were lower in the scalp hair and blood, but higher in the urine samples of hypertensive patients. The deficiency of Zn and Se and the high exposure of toxic metals may be synergistic with risk factors associated with hypertension.     

COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations

MOTIVATION: Determining orthology relations among genes across multiple genomes is an important problem in the post-genomic era. Identifying orthologous genes can not only help predict functional annotations for newly sequenced or poorly characterized genomes, but can also help predict new protein-protein interactions. Unfortunately, determining orthology relation through computational methods is not straightforward due to the presence of paralogs. Traditional approaches have relied on pairwise sequence comparisons to construct graphs, which were then partitioned into putative clusters of orthologous groups. These methods do not attempt to preserve the non-transitivity and hierarchic nature of the orthology relation. RESULTS: We propose a new method, COCO-CL, for hierarchical clustering of homology relations and identification of orthologous groups of genes. Unlike previous approaches, which are based on pairwise sequence comparisons, our method explores the correlation of evolutionary histories of individual genes in a more global context. COCO-CL can be used as a semi-independent method to delineate the orthology/paralogy relation for a refined set of homologous proteins obtained using a less-conservative clustering approach, or as a refiner that removes putative out-paralogs from clusters computed using a more inclusive approach. We analyze our clustering results manually, with support from literature and functional annotations. Since our orthology determination procedure does not employ a species tree to infer duplication events, it can be used in situations when the species tree is unknown or uncertain. CONTACT: jothi@mail.nih.gov, przytyck@mail.nih.gov SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.     

Correlation of Calcium and Magnesium Levels in the Biological Samples of Different Types of Acute Leukemia Children

We aimed to investigate the effect of maternal exposure to NaF on mandibular bone microarchitecture and phosphocalcic plasma parameters of the offspring. For this purpose, 10-, 15-, and 21-day-old pups (n?=?6–8 per group) from two groups of mothers, control and NaF 50mg/L treated dams, were used. Plasma calcium (Ca) and phosphorus (P) levels and alkaline phosphatase activity (ALP) were measured. Fluoride concentration (F^?) in bone and in stomach content was measured using potentiometry after isothermal distillation. Morphometric, histological, and histomorphometric analyses of the jaw bones were performed. Plasma Ca and P levels and ALP activity increased in 10-day and decreased in 21-day-old pups from NaF-treated mothers. Fluoride concentration in stomach content samples of 15- and 21-day-old nursing pups from mothers exposed to NaF in their drinking water was higher compared to that observed in control dam offspring. Mandibular F^? content was higher in 21-day-old pups born to F^?-exposed dams compared to those observed in age-matched control pups. Mandibular area increased in 21-day-old pups born to treated mothers as compared to controls. Mandibular bone volume BV/TV (%) was higher in offspring from NaF-exposed dams than in controls at all the studied times. The increase in bone volume after exposure to F^? was concomitant with the increase in trabecular thickness and the decrease in trabecular separation. Altogether, our results showed that exposure to NaF during gestation and lactation increased mandibular area and bone volume of pups, with concomitant changes in phosphocalcic parameters associated with the bone modeling process.     

Embryology ofCordia sebestena (Boraginaceae)

Sporogeneses and gametogeneses inCordia sebestena are described. Anther wall develops according to the Dicotyledonous type. Pollen grains are three-celled at the time of dehiscence. The occurrence of enlarged, precociously developing, densely cytoplasmic cells toward the proximal end of the anther and between adjacent pollen sacs is a unique feature in this species. The possible functions of these cells are discussed. A placental obturator develops simultaneously with the ovules. The dual origin of parietal tissue (from nucellar epidermis and the archesporial initial) is an unusual feature in this species. Megagametophyte development is monosporic or (occasionally) bisporic. Megaspore tetrads are linear or T-shaped. Double dyads and tetrads are frequently observed.—Maintainance of subfamily status forCordioideae is supported.     

CYTOEMBRYOLOGY OF ALLIUM TEXTILE NELS. & MACBR.

Root tip mitosis, meiosis, sporogeneses, and the development of gametophytes are described for eight populations of Allium textile Nels. & Macbr., native to Montana. The basic chromosome number is n = 7, with tetraploids being predominant. Of the eight populations studied, only one was composed entirely of diploids (2n = 14). Meiosis is generally normal with bivalents and tetravalents formed during the process. Laggard chromosomes leading to the formation of micronuclei are frequently observed during microsporogeny. The anther wall is five-layered and its development corresponds to the Monocotyledonous type. The tapetum is glandular and its cells remain uninucleate throughout microsporogeny. The adjacent anther locules coalesce before dehiscence. Pollen grains are shed at the three-celled stage. A stomium is organized. Ovules are anatropous, tenuinucellar and bitegminal. The archesporial cell develops directly into a megasporocyte. Development of the female gametophyte is bisporic and corresponds to the Allium type. These observations support Traub's classification (1975) on Allium.