Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

Some biological and genomic properties of rice tungro bacilliform badnavirus and rice tungro spherical waikavirus from Nepal

A survey of rice fields during the main growing seasons in 81 locations from 21 districts of the Southern Terai region of Nepal indicated that rice tungro was primarily restricted to the Hardinath (Janakpur) and Parwanipur (Bara) regions. The tungro incidence in Hardinath ranged from 17% to 51% and in Parwanipur from 6% to 61% causing about 89% grain yield loss in Hardinath. Both rice tungro bacilliform badnavirus (RTBV) and rice tungro spherical picornavirus (RTSV) were found in tungro isolates collected from Hardinath and Parwanipur. These isolates were transmitted by Nephotettix virescens and leaf extracts reacted to antisera against RTBV and RTSV. In a dot blot hybridisation assay, leaf extracts of 12 weed species collected from the tungro-affected area in Hardinath and Parwanipur also reacted with RTBV DNA probes. On mass inoculation of 15 popular rice cultivars most became more than 50% infected and only cv. Radha 9 had low (22.2%) infection. RTBV DNA and the coat protein region of RTSV from the Hardinath isolate were cloned and partially characterised. A comparative analyses by restriction endonuclease digestion, cross hybridisation, the polymerase chain reaction and partial sequencing indicated that the Nepalese RTBV DNA clone and the cDNA clones of the RTSV RNA were more similar to the various tungro isolates from the Indian subcontinent than to those from the Philippines.     

Ultrastructure and Cytochemistry of the Cell-types in the Tumorous Hematopoietic Organs and the Hemolymph of the Mutant Lethal (1) Malignant Blood Neoplasm (l(1)mbn) of Drosophila Melanogaster

The fine structure and histochemistry of the neoplastic primordial blood cell-types in the larval hematopoietic organs and the mature cell-types in the hemolymph of the blood tumor mutant lethal (1) malignant blood neoplasm (l(1) mbn ) of Drosophila melanogaster were investigated. In this mutant the cell-types of the plasmatocyte-line are neoplastic while the cell-types of the crystal-cell-line are not and are much reduced in numbers (1, 2).
In contrast to the wild-type the mutant hematopoietic organs are enlarged and contain, in addition to primordial blood-cells, large numbers of mature plasmato-, podo-, and lamellocytes.
All cell-types of the plasmatocyte-line differ in their fine structure and behavior from their wild-type counterparts. The mutant blood cells show generally a numerical increase of cell organelles and acid phosphatase positive primary and secondary lysosomes. In the phenol oxidase test they showed a vigorous melanization reaction. Plasmato- and podocytes invade into the tissues of the larva and show high phagocytic activity.     

Ultrastructure and Cytochemistry of the Cell Types in the Larval Hematopoietic Organs and Hemolymph of Drosophila Melanogaster

The ultrastructure of the primordial blood cells in the first and second hematopoietic lobes of the late second and third instar larva and prepupa of Drosophila melanogaster was compared with the ultrastructure of the blood cells found freely in the larval hemolymph. Within the hematopoietic lobes two principal cell-types were detected: (i) the prohemocytes and proplasmatocytes, and (ii) different developmental stages of crystal cells., Prohemocytes are characterized by a ribsome-rich cytoplasm, showing small amounts of mitochondria, rough ER and Golgi complexes and few primary lyosomes. Prohemocytes differentiate into proplasmatocytes. When released into the hemolymph they transform further into plasmato-, podo-, and lamellocytes. This differentiation pathway is characterized by a gradual, numerical increase of cytoplasmic organelles, the development of the lysosomal system and the aquisition of the capacity for phagocytosis and melanin formation. The differentiation of a procrystal cell into a crystal cell involves a number of intermediate stages, during which the crystalline material is produced, accumulated, and crystallized. Primary and secondary lysosomes in the primordial blood cells of the hematopoietic organs as well as the free blood cells in the hemolymph were identified cytochemically with the help of the acid phosphatase test. The capacity for melanin synthesis was studied with the phenol- and polyphenol oxidase test.     

冬虫夏草菌和蛹虫草菌的研究现状、问题及展望

冬虫夏草菌和蛹虫草菌是两种最著名的虫草菌。从分类学地位、分布、生活史及有性生殖类型、寄主范围、遗传多样性、分子遗传学和基因组学、生态学、人工栽培及产品开发等方面对冬虫夏草菌和蛹虫草菌的研究现状进行总结,指出了研究中存在的一些问题,并对研究前景进行展望。     

Sugar demand of ripening grape berries leads to recycling of surplus phloem water via the xylem

We tested the common assumption that fleshy fruits become dependent on phloem water supply because xylem inflow declines at the onset of ripening. Using two distinct grape genotypes exposed to drought stress, we found that a sink‐driven rise in phloem inflow at the beginning of ripening was sufficient to reverse drought‐induced berry shrinkage. Rewatering accelerated berry growth and sugar accumulation concurrently with leaf photosynthetic recovery. Interrupting phloem flow through the peduncle prevented the increase in berry growth after rewatering, but interrupting xylem flow did not. Nevertheless, xylem flow in ripening berries, but not berry size, remained responsive to root or shoot pressurization. A mass balance analysis on ripening berries sampled in the field suggested that phloem water inflow may exceed growth and transpiration water demands. Collecting apoplastic sap from ripening berries showed that osmotic pressure increased at distinct rates in berry vacuoles and apoplast. Our results indicate that the decrease in xylem inflow at the onset of ripening may be a consequence of the sink‐driven increase in phloem inflow. We propose a conceptual model in which surplus phloem water bypasses the fruit cells and partly evaporates from the berry surface and partly moves apoplastically to the xylem for outflow.     

Characterization of microsatellite loci in the western tarnished plant bug,Lygus hesperus Knight (Hemiptera: Miridae)

A microsatellite‐enriched partial genomic DNA library of Lygus hesperus was generated and screened by sequencing. Ten polymorphic microsatellite marker loci were characterized by genotyping 92 insect samples. The observed number of alleles ranged from three to seven with an average of 4.5 (SE ± 0.45), while the effective number of alleles ranged from 1.21 to 3.02 with an average of 2.14 (SE ± 0.20). Significant deviations from Hardy–Weinberg expectations were detected at three loci. Significant linkage disequilibrium was also detected between the loci LhMS2‐54 and LhMS3‐32. Seven of the L. hesperus markers could be transferred to Lygus lineolaris.     

Vacuolated plant cells as ideal osmometer: reversibility and limits of plasmolysis, and estimation of protoplasm volume in control and water-stress-tolerant cells

Abstract. The osmotic behaviour of vacuolated plant cells (adaxial epidermal cells of Allium cepa bulb scales, and epidermal as well as chloroplast containing subepidermal stem base cells of Pisum sativum) was studied over a wide range of CaCl₂ concentrations. The following results were obtained.

• a. Allium cepa and Pisum sativum plant cells behave as an ideal osmometer as far as plasmolytic contraction of the protoplast is concerned.
• b. The protoplasts of these cells could be plasmolysed to 15–45% of their original volume without the loss of membrane semi-permeability.
• c. Cells plasmolysed in 1.0 kmol m^?3 CaCl₂ could be completely deplasmolysed and upon deplasmolysis the cells resumed protoplasmic streaming.
• d. The above findings (a-c) indicate that during gradual plasmolysis and deplasmolysis membrane semi-permeability is maintained.
• e. At very high plasmolysing concentrations vacuoles covered with the tonoplast separated from the rest of the protoplasm in some cells whereas others showed systrophy. Extruded vacuoles were able to respond to osmotic shrinkage.
• f. The non-solvent space in Allium cells of about 3% also corresponded to the protoplasm volume calculated from the protoplast geometry (mean from results of direct measurement method and subtraction method).
• g. Subepidermal stem base cells of water-stress-tolerant Pisum plants had a 75% greater non-solvent space than the control cells indicating that a water-stress-tolerant cell may contain a larger amount of protoplasm and/or a vacuole with a higher content of colloidal material in the vacuole.
• h. Water-stress-tolerant cells showed greater tolerance to osmotic dehydration (volume reduction) than control cells.

     

On simultaneous transport of water and solute through plant cell membranes: Evidence for the absence of solvent drag effect and insensitivity of the reflection coefficient

The simultaneous efflux of tritiated water and ¹⁴C labelled ethanol from inner epidermal cells of the bulb scale of Allium cepa was measured with a specially designed efflux chamber. It was found that water and ethanol moved essentially independently. Rates of efflux of tritiated water and ¹⁴C ethanol were essentially the same in the presence or absence of a simultaneous influx of water. Using the same technique the efflux of tritiated water from the epidermal cells was measured during a simultaneous flow of nonlabelled ethanol. When tritiated water and ethanol moved in opposite directions, the water permeability values became slightly reduced depending upon the concentration of ethanol. When ethanol and tritiated water moved in the same direction, however, no effect on water permeability values could be detected. These results are best explained by the molecular theory of diffusion across lipid bilayer membranes, and are consistent with the above findings of lack of interaction between water and ethanol as they are transported across the cell membrane. In another study, the solute permeability coefficients (K_s) for non-electrolytes such as urea and methyl urea were measured by plasmolyzing the epidermal cells and transferring them to equimolal solutions of urea and methyl urea. This method was also used to measure the reflection coefficient (σ) for these nonelectrolytes. The K_s values for methyl urea were 16 times greater than the ones for urea. The values of σ for both of these solutes, however, were very close to 1. Using the K_s data available in the literature for the subepidermal cells of the Pisum sativum stem basis, the σ values were calculated for malonamide, glycerol, methyl urea, ethyl urea, dimethyl urea, and formamide. Again the K_s values for these nonelectrolytes varied by several orders of magnitude, whereas all σ values were found to be close to 1. These findings point out that σ is an insensitive parameter and that K_s, the solute permeability constant, has to be used for characterizing solute transport through the membrane. The present study shows that fast (e.g. ethanol, formamide) as well as slowly permeating molecules do not interact with water as they are transported across the cell membrane. Aqueous pores for the simultaneous transport of water and solutes, therefore, are absent in the plant cell membranes investigated here.     

Alterations in membrane transport properties by freezing injury in herbaceous plants:

Leakage of ions from a thawed tissue is a common phenomenon of freezing injury. This leakage is usually assumed to be due to loss of membrane semipermeability or membrane rupture by freezing injury. Freeze injured, yet living, onion (Allium cepa L.) epidermal cells were used to study alterations in cell membranes that result in leakage of ions. In spite of a large efflux of ions, freeze injured cells could be plasmolysed and they remained plasmolysed for several days just like the unfrozen control cells. Injured cells also exhibited protoplasmic streaming. Passive transport of KCl, urea and methyl urea across the cell membranes of injured and control cells was also studied. No difference could be detected for the transport rates of urea and methyl urea between control and injured cells. However, a dramatic increase in the transport rate of KCl was found for the injured cells. Depending upon the extent of initial freezing injury, an increase or a decrease in injury symptoms was found in the post-thaw period. During the progress of freezing injury, 10 days after thawing, a swelling of the protoplasm was seen in the irreversibly injured cells. In spite of this swelling, these cells could be plasmolysed. It appears that the high amount of K⁺ that leaks out into the extracellular water, due to freezing injury, causes protoplasmic swelling by replacing Ca²⁺ in the plasma membrane. We conclude that protoplasmic swelling is a sign of secondary injury. The results presented in this study show that membrane semipermeability is not completely lost and membrane rupture does not occur during the initial stage of freezing injury. In fact, the cells have the ability to repair damage depending upon the degree of injury. Our results show there are specific alterations in membrane semipermeability (e.g., transport of K⁺) which could be repaired completely depending on the degree of injury. These findings suggest that ion leakage due to freezing injury is due to alteration in the membrane proteins and not in the membrane lipids.