EFFECT OF VARIETAL DIFFERENCES AND POLISHING OF RICE ON QUALITY PARAMETERS OF IDLI

The effect of varietal differences and polishing of rice on quality parameters of “idli,” an Indian fermented product, were studied. In addition, the functional properties of decorticated (whole and split) black gram (Phaseolus mungo Roxb.), were also determined. Two varieties of raw rice, “Jaya” and “Minilong,” and one variety of parboiled rice “Ponni” with two degrees of polishing (high and low) were selected. Idlis were prepared following standard procedures. Variations were observed in water and fat absorption capacities of two black gram samples. Emulsification capacity ranged from 102 to 110 mL/100 g. Foam capacities at different pH range were similar, but foam stability differed as a function of time. The pH of the fermented batter was between 4.1 and 4.8. Rice with a lesser degree of polishing fermented better with higher batter volume and microbial count, lesser shear value and gave softer idlis. However, sensory analysis revealed that idlis prepared with low‐polish rice scored significantly lower for appearance and color quality compared with products prepared with high‐polish rice. Significant differences were observed in the quality of flavor of all products. It can be concluded that the quality characteristics of Idli were influenced by the variety of rice and the degree of polishing, but the two types of black gram used, whole and split, had no effect.     

Sequence polymorphisms in wild,weedy, and cultivated rice suggest seed‐shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed‐shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ~26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.     

CELL SIZE DIFFERENTIATION IN THE BLOOM-FORMING DINOFLAGELLATE GYMNODINIUM CF. NAGASAKIENSE1

Two subpopulations differing essentially by their mean cell size were observed regularly in cultures and natural samples of the naked dinoflagellate Gymnodinium cf. nagasakiense Takayama et Adachi (currently known as Gyrodinium aureolum Hulburt), a species which frequently forms red tides in North European seas. “Large” cells represented the typical forms; they were morphologically similar to cells of the closely related Japanese species G. nagasakiense, which did not form any subpopulation of reduced size. “Small” and “large” cells of G. cf. nagasakiense had the same DNA content, but the nucleus of the former appeared to be much more condensed during interphase. Each cell type was able to divide and had its own growth dynamics; therefore, any intermediary between pure populations of “small” and of “large” cells were observed in culture. The “large” form generated a “small” cell by an atypical budding-like division, whereas the “small” form gave back a “large” form, once it ceased to divide, by simple enlargement of its cell body. Factory inducing cell size differentiation are yet unclear. Neither nitrogen nor phosphorus starvation induced a significant increase in the relative proportion of “small” and budding cells. Although cell size differentiation is associated with the formation of gametes in a variety of dinoflagellates, we demonstrated that “small” cells of G. cf. nagasakiense are able to divide asexually, in contrast to gametes of most other species. The high proliferative power of “small” cells as compared with normal cells suggests that they could play a significant role during red tides of G. cf. nagasakiense; in contrast, cells of the Japanese species G. Nagasakiense could sustain high growth rates with larger cell size because this species generally blooms in waters much warmer than those found in northern Europe.     

Salt‐Treated Roots of Oryza australiensis Seedlings are Enriched with Proteins Involved in Energetics and Transport

Salinity is a major constraint on rice productivity worldwide. However, mechanisms of salt tolerance in wild rice relatives are unknown. Root microsomal proteins are extracted from two Oryza australiensis accessions contrasting in salt tolerance. Whole roots of 2‐week‐old seedlings are treated with 80 mM NaCl for 30 days to induce salt stress. Proteins are quantified by tandem mass tags (TMT) and triple‐stage Mass Spectrometry. More than 200 differentially expressed proteins between the salt‐treated and control samples in the two accessions (p‐value <0.05) are found. Gene Ontology (GO) analysis shows that proteins categorized as “metabolic process,” “transport,” and “transmembrane transporter” are highly responsive to salt treatment. In particular, mitochondrial ATPases and SNARE proteins are more abundant in roots of the salt‐tolerant accession and responded strongly when roots are exposed to salinity. mRNA quantification validated the elevated protein abundances of a monosaccharide transporter and an antiporter observed in the salt‐tolerant genotype. The importance of the upregulated monosaccharide transporter and a VAMP‐like protein by measuring salinity responses of two yeast knockout mutants for genes homologous to those encoding these proteins in rice are confirmed. Potential new mechanisms of salt tolerance in rice, with implications for breeding of elite cultivars are also discussed.     

The function of three main call types in common cuckoo

Acoustic signals play a key role in shaping the relationships in birds. Common cuckoos Cuculus canorus are known to produce various call types, but the function of these calls has only been studied recently. Here, we used a combination of field recordings (conducted in 2017) and playback experiments (conducted in 2018) to investigate the functional significance of common cuckoo calls. We found significant differences in the characteristics between male two‐element “cu‐coo” and three‐element “cu‐cu‐coo” calls, with these two call types being used in different contexts. The three‐element male “cu‐cu‐coo” calls were associated with females emitting their “bubbling” call. Playback experiments revealed that both males and females exhibit stronger responses to playing female “bubbling” calls than with the calls of the Eurasian sparrowhawk (Accipter nisus) serving as a control, suggesting a significant intraspecific communication function for this call type. However, we did not find any evidence to support mate attraction in male calls, as females were not stimulated by playback of male calls compared with sparrowhawk calls in the control group.     

Developmental Changes in the Structure of Endosperm Starch of Rice (Oryza sativa L.)

The developmental changes in the structure and properties of endosperm starches were investigated using the near-isogenic lines for wx alleles of rice. The amylose content in nonwaxy starch was increased during the development of rice grains. Because the accumulation of amylose in endosperm stopped earlier than that of amylopectin during development, the percentages of amylose reached a maximum at the 17th day after flowering in nonwaxy endosperm. Since the distributions of the unit-chain length of amylopectin in waxy and nonwaxy starches were unchanged with the development of the grains, these amylopectins would be synthesized in a similar manner through development. The structure and properties of endosperm starches were reconfirmed to be conspicuously affected by the temperature at the early developmental stages of the grain-filling period, namely, they appeared to be characterized by the temperature at which the starch was accumulated in the endosperm.     

Abundance and Structure Composition of nirK and nosZ Genes as Well as Denitrifying Activity in Heavy Metal-polluted Paddy Soils

Denitrification is an important microbial process in soils and leads to the emission of nitrous oxide (N₂O). However, studies about the microbial community involved in denitrification processes in polluted paddy fields are scarce. Here, we studied two rice paddies which had been polluted for more than three decades by metal mining and smelter activities. Abundance and community composition were determined using real-time polymerase chain reaction (PCR) assay and denaturing gradient gel electrophoresis of nitrite reductase and nitrous oxide reductase gene amplicons (nirK and nosZ), while denitrifying activities were assessed by measuring potential denitrifier enzyme activity. We found that the community structure of both nirK and nosZ containing denitrifiers shifted under pollution in the two rice paddies. All the retrieved nirK sequences did not group into either α- or β-proteobacteria, while most of the nosZ species were affiliated with α-proteobacteria. While the abundance of both nirK and nosZ was significantly reduced in the polluted soils at “Dexing” (with relatively higher Cu levels), these parameters did not change significantly at “Dabaoshan” (polluted with Cd, Pb, Cu, and Zn). Furthermore, total denitrifying activity and N₂O production and reduction rates also only decreased under pollution at “Dexing.” These findings suggest that nirK and nosZ containing denitrifier populations and their activities could be sensitive to considerable Cu pollution, which could potentially affect N₂O release from polluted paddy soils.     

PHYLOGENETIC AFFINITIES OF “CHANTRANSIA” STAGES IN MEMBERS OF THE BATRACHOSPERMALES AND THOREALES (RHODOPHYTA)1

This study evaluated the phylogenetic relationship among samples of “Chantransia” stage of the Batrachospermales and Thoreales from several regions of the world based on sequences of two genes—the plastid‐encoded RUBISCO LSU gene (rbcL) and the nuclear SSU ribosomal DNA gene (SSU rDNA). All sequences of “Chantransia macrospora” were shown to belong to Batrachospermum macrosporum based on both molecular markers, confirming evidence from previous studies. In contrast, nine species are now associated with “Chantransia pygmaea,” including seven species of the Batrachospermales and two of the Thoreales. Therefore, the presence of “C. macrospora” in a stream can be considered reliable evidence that it belongs to B. macrosporum, whereas the occurrence of “C. pygmaea” does not allow the recognition of any particular species, since it is associated with at least nine species. Affinities of “Chantransia” stages to particular taxa were congruent for 70.5% of the samples comparing the rbcL and SSU analyses, which were associated with the same or closely related species for both markers. Sequence divergences have been reported in the “Chantransia” stage in comparison to the respective gametophyte, and this matter deserves further attention.     

Differential Sensitivity of Macrocarpa and Microcarpa Types of Chickpea （Cicer arietinum L.） to Water Stress： Association of Contrasting Stress Response with Oxidative Injury

Chickpea (Cicer arietinum L.) is particularly sensitive to water stress at its reproductive phase and, under conditions of water stress, will abort flowers and pods, thus reducing yield potential. There are two types of chickpea: (i) Macrocarpa (“Kabuli”), which has large, rams head‐shaped, light brown seeds; and (ii) Microcarpa (“Desi”), which has small, angular and dark‐brown seeds. Relatively speaking, “Kabuli” has been reported to be more sensitive to water stress than “Desi”. The underlying mechanisms associated with contrasting sensitivity to water stress at the metabolic level are not well understood. We hypothesized that one of the reasons for contrasting water stress sensitivity in the two types of chickpea may be a variation in oxidative injury. In the present study, plants of both types were water stressed at the reproductive stage for 14 d. As a result of the stress, the “Kabuli” type exhibited an 80% reduction in seed yield over control compared with a 64% reduction observed for the “Desi” type. The decrease in leaf water potential (Ψ_w) was faster in the “Kabuli” compared with the “Desi” type. At the end of the water stress period, Ψ_w was reduced to ?2.9 and ?3.1 MPa in the “Desi” and “Kabuli” types, respectively, without any significant difference between them. On the last day of stress, “Kabuli” experienced 20% more membrane injury than “Desi”. The chlorophyll content and photosynthetic rate were significantly greater in “Desi” compared with “Kabuli”. The malondialdehyde and H₂O₂ content were markedly higher at the end of the water stress in “Kabuli” compared with “Desi”, indicating greater oxidative stress in the former. Levels of anti‐oxidants, such as ascorbic acid and glutathione, were significantly higher in “Desi” than “Kabuli”. Superoxide dismutase and catalase activity did not differ significantly between the two types of chickpea, whereas on the 10th day, the activities of ascorbate peroxidase, dehydroascorbate reductase, and glutathione reductase were higher in “Desi”. These findings indicate that the greater stress tolerance in the “Desi” type may be ascribed to its superior ability to maintain better water status, which results in less oxidative damage. In addition, laboratory studies conducted by subjecting both types of chickpea to similar levels of polyethylene glycol‐induced water stress and to 10 μ.mol/L abscisic acid indicated a greater capacity of the “Desi” type to deal with oxidative stress than the “Kabuli” type. (Managing editor: Ping He)     

Identification of germinal disk region derived genes potentially involved in hen fertility

Despite the regular decrease in fertility observed in hens, especially in “meat” lines, little is known about genes affecting fertility. We used the Affymetrix microarray to search for oocyte genes whose expression would vary in relation to fertility rate in both “laying” and “meat” line hens. We focused on oocyte genes because several of them have been found to be involved in fertility in other species. Based on microarray analysis, 54 and 84 genes were differentially expressed between germinal disc regions (GDR) of F1 maturation stage oocytes from hens exhibiting either high (100%) or low (from 22% to 80%) fertility rate from laying and meat lines respectively. Most of these differentially expressed genes were distributed between “laying” and “meat” lines indicating that mechanisms involved in the decrease in fertility rates in these two cases were independent. Real time RT‐PCR performed on the same samples which were used for microarray confirmed in several cases differences in gene expression levels detected by microarray. Moreover the correlations between gene expression levels and fertility rates were evaluated for the 10 most interesting genes at different stages of follicular maturation and early embryo development on individual GDR samples from hens exhibiting different fertility rates. In total, we identified five genes whose expression levels correlated with fertility rate in accordance with findings of microarray analysis and real time RT‐PCR: VWC2, CR407412, TAPA, FGL2, and TRAP6. The biological significance of these genes sheds light on potential mechanisms influencing fertility and could provide candidates for fertility markers in the hen. Mol. Reprod. Dev. 76: 1043–1055, 2009. © 2009 Wiley‐Liss, Inc.     

Multiple Forms of Polyglucoside-Branching Enzyme in the Algae

Three isozymes specifically concerned with the “branching” of linear polyglucosides have been delected in algae. These enzymes were detected using two-dimensional polyacrylamide gel electrophoresis, and were found to be present in blue-green, red and in green algae. Two isozynies were found in Oscillatoria princeps; three enzymes were present in Spirogyra setiformis, and two and three such enzymes were detected in red algae of the Rhodymenia type. The significance of the multiple forms of this branching enzyme was assessed in light of the type of storage poly-glucosides formed by these plants. The “degree of branching” of the storage sugar appeared to be related to the evolutionary status of these algae.     

Trypan blue as a fluorochrome for confocal laser scanning microscopy of arbuscular mycorrhizae in three mangroves

Roots of three mangroves, Acanthus ilicifolius, Ceriops tagal and Excoecaria agallocha, collected from forests of the Sundarbans of India were stained with trypan blue to observe arbuscular mycorrhizal colonization. Spores of arbuscular mycorrhizal fungi isolated from rhizospheric soil, collected together with the root samples, also were stained for testing the suitability of the dye as a fluorochrome. Confocal laser scanning microscopy images were constructed. A. ilicifolius and E. agallocha exhibited “Arum” type colonization with highly branched arbuscules, whereas C. tagal showed “Paris” type association with clumped and collapsed arbuscules. We demonstrated that trypan blue is a suitable fluorochrome for staining arbuscular mycorrhizal fungal spores, fungal hyphae, arbuscules and vesicles, which presumably have a considerable amount of surface chitin. It appears that as the integration of chitin into the fungal cell wall changes, its accessibility to trypan blue dye also changes.     

First fungus gnats of genus Manota Williston (Diptera: Mycetophilidae) from Japan

The genus Manota is recorded from Japan for the first time. Three new species, Manota satoyamanis, Manota indahae and Manota tunoae spp. nov., are described, based on specimens collected in an ecological sampling program of arthropods in the “satoyama” landscape of Ishikawa Prefecture. “Satoyama” represents the traditional rural landscape of Japan, which is characterized by a mosaic of secondary forests, plantations, ponds and rice paddy fields. The new species raise the number of Palearctic Manota species from five to eight.     

Structures of Arg‐ and Gln‐type bacterial cysteine dioxygenase homologs

In some bacteria, cysteine is converted to cysteine sulfinic acid by cysteine dioxygenases (CDO) that are only ～15–30% identical in sequence to mammalian CDOs. Among bacterial proteins having this range of sequence similarity to mammalian CDO are some that conserve an active site Arg residue (“Arg‐type” enzymes) and some having a Gln substituted for this Arg (“Gln‐type” enzymes). Here, we describe a structure from each of these enzyme types by analyzing structures originally solved by structural genomics groups but not published: a Bacillus subtilis “Arg‐type” enzyme that has cysteine dioxygenase activity (BsCDO), and a Ralstonia eutropha “Gln‐type” CDO homolog of uncharacterized activity (ReCDOhom). The BsCDO active site is well conserved with mammalian CDO, and a cysteine complex captured in the active site confirms that the cysteine binding mode is also similar. The ReCDOhom structure reveals a new active site Arg residue that is hydrogen bonding to an iron‐bound diatomic molecule we have interpreted as dioxygen. Notably, the Arg position is not compatible with the mode of Cys binding seen in both rat CDO and BsCDO. As sequence alignments show that this newly discovered active site Arg is well conserved among “Gln‐type” CDO enzymes, we conclude that the “Gln‐type” CDO homologs are not authentic CDOs but will have substrate specificity more similar to 3‐mercaptopropionate dioxygenases.     

Alkaliviscogram and Other Properties of Starch of Tropical Rice

In the alkaliviscogram of starch of 26 nonwaxy rices grown in the tropics, gelatinization normality correlated positively with final gelatinization temperature (BEPT) of starch (r=0.969^**) and negatively with alkali spreading value of milled rice (r= ?0.931^**). Peak viscosity was not linearly related to amylose content. Among samples of rice starch having a high amylose (>28%) content, peak viscosity was correlated with the gel consistency of starch (r=?0.690^**) and of milled rice (r=?0.644^**) (n = 18). These high-amylose starches showed the widest variation in peak viscosity. Amylose content, and gel consistency were inherited from the same parent in all nine varieties and lines studied, whereas peak viscosity, gelatinization normality and the final BEPT were inherited from either parent. The starch of five waxy rices showed higher peak viscosities even at a concentration of 1.8% as compared with a 2.0% nonwaxy rice starch.     

Five classes of visual interneurons in the optic nerve of the hermit crab

Response characteristics and trigger features are described for five operational classes of visual interneurons in the optic nerve of the hermit crab. The units were initially segregated on the basis of response sign (“on”, “off”, “on-off”) and duration (phasic, tonic). Tonic “on” and tonic “off” units were observed to be indistinguishable from the previously described sustaining and dimming fibers of other decapod crustacea. Phasic “off” units closely resemble either jittery motion or novelty detectors also previously documented. Phasic “on” units are characterized by an excitable antagonistic surround, a slow rate of habituation, and a sustained low level discharge during periods of increasing luminous flux at any point within their receptive fields. Highly sensitive to moving contours, they occasionally revealed a directional preference. The phasic “on” units are also capable of following brief stimuli at rates of up to 20/sec. Phasic “on-off” units were characterized by coextensive receptive fields for “on” and “off” responses and movement sensitivity independent of contrast.     

Isolation and Identification of Pythiaceous Fungi from Irrigation Water and their Pathogenicity to Antirrhinum, Tomato and Chamaecyparis lawsoniana

Pythiaceous fungi were isolated from irrigation water using a variety of natural and artificial baits. Isolates were also obtained by plating water samples directly on the surface of selective agar media. The selective medium of Ocana and Tsaq (1966) PlOVP, was modified by substituting rifampicin and ampicillin (10 and 500 μg cm^?3 respectively) for vancomycin to suppress bacterial growth from water samples. The pythiaceous fungi were identified as Pythiitm dissotocitm, P. middletonii, P. mamillatum, P. rostratum, Pythium“group 1”, “group 2” and “group 3” and Phytophtbom gona-podyides. All isolates of P. gonapodyides were the A1 strain and produced oospores when paired with an A2 isolate of P. drechsleri. Isolates were tested for their pathogenicity to Antirrhinum, tomato and Chatmaecyparis lawsoniana cv. Ellwoodii. Pythium middletonii and Pythium“group 1” caused severe pre-emergence damping-off of Antirrhinum seedlings, P. mamillatuni, P. rostratum and Pythium“group 3” were less pathogenic to the same host while P. dissotocum, Pythium“group 2” and Phytophthora gonapodyides were non-pathogenic. Only isolates of Pythium“group 1” were pathogenic to tomato seedlings. None of the fungi was pathogenic to rooted cuttings of Chamaecyparis lawsoniana cv. Ellwoodii.     

Geminivirus transmission and biological characterisation of Bemisia tabaci (Gennadius) biotypes from different geographic regions

Eighteen populations of Bemisia tabaci, collected from different geographic locations (North & Central America, the Caribbean, Africa, the Middle East, Asia and Europe), were studied to identify and compare biological and genetic characteristics that can be used to differentiate biotypes. The morphology of the fourth instar/pupal stage and compound eye structures of adults were investigated using scanning electron microscopy and found to be typical of the species among all biotypes and populations studied. Setae and spines of B. tabaci larval scales from the same colony were highly variable depending on the host plant species or leaf surface characteristics. The location and the morphology of caudal setae, characteristic of all B. tabaci studied to date, were present in all colonies. However, differences in adult body lengths and in the ability to induce phy to toxic disorders in certain plant species were found between biotypes or populations. The recently identified “B” biotype, characterised by a diagnostic esterase banding pattern and by its ability to induce phytotoxic responses in squash, honeysuckle and nightshade was readily distinguished from non-“B” biotype populations. None of the non-“B” biotypes studied, were found to induce phytotoxic responses. Nine populations examined showed typical “B” biotype characteristics, regardless of country of origin. All tested populations, determined as “B” or “B”-like biotypes successfully mated with other “B” biotype colonies from different geographic areas. Non-“B” biotype colonies did not interbreed with other biotypes. The B. tabaci populations were tested for their ability to transmit 15 whitefly-transmitted geminiviruses (WTGs) from different geographic areas with a wide range of symptom types. All WTGs were transmitted by the “B” biotype colonies and by most non-“B” biotype colonies, with the exception of three viruses found in ornamental plants which were non-transmissible by any colony. Some non-“B” biotypes would not transmit certain geminiviruses and some geminiviruses were more efficiently transmitted than were others.