Length–weight and length–length relationships of four species of genus Pethia and genus Puntius from wetlands of Lakhimpur district,Assam, India

Length–weight relationships (LWR) and length–length relationships (LLR) were estimated for four species, namely, Puntius sophore (Hamilton, 1822), Puntius chola (Hamilton, 1822), Pethia ornatus (Vishwanath & Laisram, 2004) and Pethia ticto (Hamilton, 1822) collected from different wetlands of Lakhimpur, Assam. The values of the parameter slope (b) in the LWR were 3.30 for Puntius sophore, 3.22 for Puntius chola, 2.61 for Pethia ornatus and 3.27 for Pethia ticto. The relationships among TL, FL and SL were all linear (r² > 0.95).     

Polymorphic microsatellite DNA markers for the white‐breasted thrasher,Ramphocinclus brachyurus

We isolated and characterized six polymorphic microsatellite markers for the white‐breasted thrasher from genomic libraries enriched for (AC)_n, (GT)_n, (CAAA)_n, (TTTC)_n, (GAC)_n, (CT)_n and (TTTG)_n microsatellites. The number of alleles per locus ranged from two to seven. Observed heterozygosity (H_O) ranged from 0.30 to 0.85.     

Reproductive and sexual characteristics in five Lethrinus species in waters off the Ryukyu Islands

Gonads of five lethrinids, viz., Lethrinus harak, L. miniatus, L. obsoletus, L. ornatus, and L. sp. 2, were collected monthly in waters off the Ryukyu Islands and observed histologically to reveal their spawning periods and size at sexual maturation and sexual transition. The spawning period was from April to November for L. harak, from April to July for L. miniatus, from April to October for L. obsoletus, from May to November for L. ornatus, and from April to October for L. sp. 2. Sexual patterns in the five species were determined by fork length at both sexual maturation and sexual transition. The body size (fork length, FL) and sex ratio (% of female) at 90% maturity in L. harak were 21.1 cm FL and 90%, respectively; those of L. miniatus were 42.2 cm FL and 80%; 25.7 cm FL and 60% for L. obsoletus; about 20 cm FL and 90% for L. ornatus; and about 26 cm FL and 90% for L. sp. 2. Because the sex ratios decreased to 0% at the maximum size classes in L. miniatus, L. ornatus, and L. sp. 2, the sexual patterns in these species were considered to be protogynous hermaphrodite. Although the sex ratio (% of female) once decreased to about 30% at 28 cm FL, rapid increase occurred in the larger size class in L. harak. However, the increase did not result from sexual transition. Hence, the sexual pattern of L. harak was considered to be protogynous hermaphrodite. Because the sex ratio (% of female) at body sizes larger than 23 cm FL was stable at about 60% in L. obsoletus, the sexual pattern was determined to be one of juvenile hermaphrodites.     

Two new decapod (Crustacea,Malacostraca) complete mitochondrial genomes: bearings on the phylogenetic relationships within the Decapoda

Recent advances in molecular phylogenetics are continuously changing our perception of decapod phylogeny. Although the two suborders Dendrobranchiata and Pleocyemata within the Decapoda are widely accepted, this taxonomic view is now challenged when using mitochondrial protein‐coding genes to investigate the decapod phylogeny, especially for the basal pleocyematan groups. Here, we enhanced taxonomic coverage by sequencing the genomes of two basal decapod taxa Alpheus distinguendus and Panulirus ornatus, representing two infraorders, Caridea and Achelata, respectively. Based on these two and other available mitochondrial genomes, we evaluated the usefulness of protein‐coding genes in resolving deep phylogenetic relationships of the Decapoda using maximum likelihood and Bayesian analyses. The mt genomic results revealed a novel gene order because of the reverse transposition of trnE (transfer, trn for Glutamate) and a pseudogene‐like trnS (AGN) [trn for Serine (S₁, AGN)] in the mitochondrial genome of A. distinguendus, and a duplicate of 89 bp sequences in the putative noncoding region of P. ornatus. Our phylogenetic inferences suggest monophyly of the Decapoda and its two suborders, and that several lineages within the Reptantia are consistently recovered with high nodal supports. Our findings suggest that the best mitochondrial genome phylogeny can be found on the premise that systematic errors should be minimized as much as possible. © 2011 The Linnean Society of London, Zoological Journal of the Linnean Society, 2011, 162 , 471–481.     

Microsatellite markers for the Mexican spotted owl (Strix occidentalis lucida)

A genomic cosmid library was used to develop seven highly polymorphic microsatellite markers for the Mexican spotted owl (Strix occidentalis lucida). These are the first reported microsatellite markers derived from this species. The cloned and sequenced repeat motifs include a triplet repeat of (AAT)_n, two tetranucleotide repeats of (GATA)_n, a tetranucleotide repeat of (ATCC)_n, a compound repeat of (GA)_n(GATA)_n and the two pentanucleotide repeats (AGAAT)_n and (ATTTT)_n. The microsatellites described represent six presumably independent loci with the two pentanucleotide repeats having originated from a single cosmid. Primer pairs allow locus‐specific amplification of each marker from Mexican spotted owl genomic DNA.     

Feeding-season production in the desert millipede Orthoporus ornatus (Girard) (Diplopoda)

Summary Production during an assumed 131-day feeding season in 1974 was estimated for Orthoporus ornatus between 4.0 and 12.0 mm in midsegment width at Tornillo Flat, Big Bend National Park, Texas.A conservative density estimate in 1973 of 1,302 millipedes ha^-1 involved daily specimen removal from three, 929-m² plots for a month. Each plot typified a different aspect of local desert vegetation; most specimens came from the plot with greatest plant diversity and relatively high (20%) cover.Production calculations using 1973 density estimates were based on increase in size-class specific dry weight (minus gut contents) between 14 May and 21 September, 1974. Production ha^-1 of cuticle and tissue was estimated at 0.85 kg (1972 kcal), while that of tissue alone came to 0.29 kg (1971 kcal). Orthoporus ornatus from Albuquerque, New Mexico increased in dry weight during 92 days in 1974 more rapidly and to a greater extent than comparable size classes at Tornillo Flat.An estimated feeding-season energy budget based on ash-free values of shrub food eaten at Tornillo Flat indicated ingestion ha^-1 of 3,434 g (13,712 kcal) and defecation of 3,181 g (9,187 kcal). An independent estimate of ingestion based on known ingestion rates was 8,851 g ha^-1.Considering probable net primary production at Tornillo Flat, local O. ornatus exert a trophic impact similar to that of other large invertebrate detritivores elsewhere.     

Theoretical π-π* absorption and circular dichroic spectra of helical poly(L-proline) forms I and II

Absorption and CD spectra of the π-π* transition near 200 nm are calculated for helical (Pro)_n I and II (n = 6, 10) using the dipole interaction model, including interactions among all atoms, with optical parameters obtained from previous studies of related molecules. Calculated spectra for (Ala)_n and (Pro)_n in the same conformation show marked differences. The spectra for (Pro)_n are sensitive to side-chain structure but are found to agree reasonably well with exeriment for forms I and II when the side-chain C? C bond length is set at 1.54 Å, with structural data otherwise obtained from x-ray diffraction studies.     

Microsatellite loci from Russula brevipes,a common ectomycorrhizal associate of several tree species in North America

Six microsatellite loci were isolated and characterized from genomic libraries enriched for (CA)_n (GA)_n (ATG)_n, and (CAG)_n, microsatellite motifs from Russula brevipes, a common ectomycorrhizal fungus that forms mutualisms with several species of trees in North America. The polymerase chain reaction primers were tested on 27 sporocarps of R. brevipes sampled in Douglas fir (Pseudotsuga menziesii), grey pine (Pinus sabiniana), and Sitka spruce (Picea sitchensis) stands. The number of alleles per locus ranged from two to 14 with expected heterozygosity values from 0.00 to 0.92 within populations. These are the first six microsatellite loci characterized from Russula brevipes that can be used for estimating genotypic diversity and population structure.     

Helix coil transitions of d (A)n·d(T)n,d(A-T)n·d(A-T)n,and d(A-A-T)n·d(A-T-T)n; evaluation of parameters governing DNA stability

The thermally induced helix-coil transitions of three A-T DNAs, d(A)_n·d(T)_n, d(A-T)_n·d(A-T)_n, and d(A-A-T)_n·d(A-T-T)_n, were studied. Experimental transition curves of the DNAs were analyzed using the loop entropy model of DNA melting. The calculation of the melting curve of d(A-A-T)_n·d(A-T-T)_n is presented using the integral equation formalism of Goel and Montroll. The aim of this work was to evaluate thermodynamic parameters which govern DNA stability and to test the theoretical model employed in the analysis. Our results show (1) an excellent over-all agreement between theory and experiment, (2) a loop entropy exponent k = 1.55 ± 0.05 provided the best fit to all the polymer transition curves, (3) the evaluated stacking free energies reflect the relative stability of the DNAs, and (4) the stacking energies of the ApA·TpT dimer evaluated from d(A)_n·d(T)_n and d(A-A-T)_n·d(A-T-T)_n differ. The last result is consistent with different conformations for the dimer in these two polymers.     

Extraction, separation and labeling with 14C-glucose of HeLa cell polyglucose, RNA and DNA and comparison of the molecular weights and buoyant densities of polyglucose from poliovirus-infected and noninfected cultures

The aqueous phase of phenol extracts of HeLa cells contains polyglucose (CHO)_n, RNA, and DNA. These macromolecules were precipitated together and removed from 50% (v/v) ethanol solutions with a stirring rod. The viscous precipitate had the classical white appearance of DNA, but contained an average of 439, 670, and 220 μg (from 3 × 10⁷ cells) of (CHO)_n, RNA, and DNA, respectively. The (CHO)_n was separated from the RNA, either by CsCl density gradient centrifugation or by precipitating the RNA with trichloroacetic acid (TCA). Both methods of separation resulted in preparations of (CHO)_n with similar specific activities (radioactive counts/μg min). However, electron micrographs showed that the (CHO)_n separated by using TCA had a greater variation in particle size when compared with (CHO)_n separated by CsCl centrifugation. With the CsCl methods, the number-average molecular weights, as determined by electron microscope particle-counting, and the buoyant densities of (CHO)_n whose synthesis was stimulated by poliovirus infection and (CHO)_n from noninfected cultures, were found to be similar. When the (CHO)_n was extracted from HeLa cells with TCA, rather than phenol, the yield was 1.68-fold greater and its specific activity was an average of twice that of the (CHO)_n extracted with phenol. The time at which cells were pulse-labeled with ¹⁴C-glucose, after reducing the glucose in the culture medium to 0.01 of normal, was found to be important, in that the specific activity of the (CHO)_n increased 23.4-fold over a 4-hr period and the amount extracted decreased 8.2-fold. The increase in the specific activities of RNA and DNA was not as large as that of the (CHO)_n and the amounts extracted were not significantly changed. The sedimentation coefficients of RNA and (CHO)_n which were separated from each other with TCA were 6.4 and 116 S, respectively, whereas, without separation, two peaks were seen, with values of 25.4 and 31.4 S. Chloride ions reduce the sensitivity of the Burton test for DNA. However, the Burton reagent will detect (CHO)_n even in the presence of DNA if the assay mixture is heated. Chloride ions increase the sensitivity of the Burton reagent to detect melizitose and, at concentrations above l.5M, synthetic- polyglucose by increasing the absorption of the colored (CHO)_n reaction product(s).     

Characterization of highly variable (GA/CT) n microsatellites in the bur oak,Quercus macrocarpa

The objective of this study was to ascertain the usefulness of polymerase chain reaction (PCR)-based microsatellite analysis for studying pollination and parentage in a wind-pollinated temperate tree. A small insert genomic library of the bur oak (Quercus macrocarpa) was constructed and screened for the presence of (CA/GT) _n and (GA/CT) _n repeats. The proportion of positive clones yielded estimates of 3×10⁵ such dinucleotide repeats per genome, roughly comparable to abundances reported in other eukaryotic genomes. Thirteen positive clones were sequenced. In contrast to mammalian genomes, the (GA/CT) _n motif was more abundant than the (CA/GT) _n motif in these clones. The (GA/CT) _n repeats also showed longer average repeat length (mean n=16.2 versus 7.3), suggesting that they are better candidates for yielding polymorphic genetic markers in oak genomes. Indeed, a survey of adult bur oaks and offspring in a small stand in northern Illinois at 3 of these (GA/CT) _n microsatellite loci revealed Mendelian inheritance and extremely high levels of polymorphism, with the number of alleles at each locus ranging from 11–20 and heterozygosity ranging from 0.66 to 0.75. These results, indicating that (GA/CT) _n microsatellites are both abundant and highly polymorphic in the bur oak genome, suggest that such genetic markers have tremendous potential for applications for studies of parentage, pollination and dispersal in temperate trees.     

Isolation and characterization of Brachymystax lenok microsatellite loci and cross‐species amplification in Hucho spp. and Parahucho perryi

We isolated and characterized eight polymorphic microsatellite markers for Brachymystax lenok (Pallas, 1773) from genomic libraries enriched for (GATA)_n, (GACA)_n and (ATG)_n microsatellites. The number of alleles per locus ranged from two to 17. Heterozygosity ranged from 0.2 to 0.95. In addition, cross‐species amplification was successful for seven loci in Hucho hucho, eight in H. taimen and seven in Parahucho perryi.     

Isolation of polymorphic tetranucleotide microsatellite markers for the streak‐necked flycatcher Mionectes striaticollis

We have isolated 11 polymorphic microsatellite markers for the streak‐necked flycatcher Mionectes striaticollis from genomic libraries enriched for either (AACC)_n, (AAGG)_n or (AAAG)_n repetitive elements. The number of alleles ranged from four to 14 per locus with the observed heterozygosity ranging from 0.38 to 1.00. These markers will be useful for analysis of questions concerning population genetic structure and models of speciation.     

Informativeness of human (dC-dA)n · (dG-dT)n polymorphisms

Abundant human interspersed repetitive DNA sequences of the form (dC-dA)_n · (dG-dT)_n have been shown to exhibit length polymorphisms. Examination of over 100 human (dC-dA)_n · (dG-dT)_n sequences revealed that the sequences differed from each other both in numbers of repeats and in repeat sequence type. Using a set of precise classification rules, the sequences were divided into three categories: perfect repeat sequences without interruptions in the runs of CA or GT dinucleotides (64% of total), imperfect repeat sequences with one or more interruptions in the run of repeats (25%), and compound repeat sequences with adjacent tandem simple repeats of a different sequence (11%). Informativeness of (dC-dA)_n · (dG-dT)_n markers in the perfect sequence category was found to increase with increasing average numbers of repeats. PIC values ranged from 0 at about 10 or fewer repeats to above 0.8 for sequences with about 24 or more repeats. (dC-dA)_n · (dG-dT)_n polymorphisms in the imperfect sequence category showed lower informativeness than expected on the basis of the total numbers of repeats. The longest run of uninterrupted CA or GT repeats was found to be the best predictor of informativeness of (dC-dA)_n · (dG-dT)_n polymorphisms regardless of the repeat sequence category.     

Chemodiversity of Nonacosan‐10‐ol and n‐Alkanes in the Needle Wax of Pinus heldreichii

This is the first report of individual variability and population diversity of the contents of nonacosan‐10‐ol and n‐alkanes in the needle cuticular waxes of Bosnian pines originated from Montenegro, regarded as Pinus heldreichii var. leucodermis, and from Serbia, regarded as P. heldreichii var. pan?i?i. The amount of nonacosan‐10‐ol varied individually from 27.4 to 73.2% (55.5% in average), but differences between the four investigated populations were not statistically confirmed. The size of the n‐alkanes ranged from C₁₈ to C₃₃. The most abundant n‐alkanes were C₂₃, C₂₇, and C₂₅ (12.2, 11.2, and 10.8% in average, resp.). The carbon preference index (CPI) of the n‐alkanes ranged from 0.8 to 3.1 (1.6 in average), while the average chain length (ACL) ranged from 20.9 to 26.5 (24.4 in average). Long‐chain and mid‐chain n‐alkanes prevailed (49.6 and 37.9% in average, resp.). It was also found that the populations of P. heldreichii var. leucodermis had predominantly a narrower range of n‐alkanes (C₁₈? C₃₁) than the trees of the variety pan?i?i (C₁₈? C₃₃). Differences between the varieties were also significant for most of the other characteristics of the n‐alkane pattern (e.g., most abundant n‐alkanes, CPI, ACL, and relative proportion of short‐, mid‐, and long‐chain n‐alkanes). The principle component and cluster analyses of eleven n‐alkanes confirmed the significant diversity of these two varieties.     

Formation and stability of helical poly(N epsilon,N epsilon,N epsilon-trimethyl-L-lysine) in sodium perchlorate solution

Poly(trimethyl-L-lysine), [Lys(Me₃)]_n, is converted from random coil to α-helix at about 1/30 of the NaClO₄ concentration required by poly(L-lysine), (Lys)_n. NaClO₄ generates turbidity in [Lys(Me)₃]_n at concentrations above that required for helix formation, and decreases turbidity above lM NaClO₄. The turbidity runs parallel to enhanced, and then decreased, fluorescence of a dansyl label. Helix formation per se does not induce enhanced fluorescence. Increasing NaClO₄ concentration increases T_m linearly with log[NaClO₄] for both (Lys)_n and [Lys(Me₃)]_n until the denaturing effect of high NaClO₄ sets in. Increasing NaClO₄ also increases the breadth of the transition. Heating helical [Lys(Me₃)]_n or (Lys)_n does not produce a CD spectrum resembling that of “random-coil” (Lys)_n, except for [Lys(Me₃)]_n at relatively low NaClO₄ concentration.     

Conformation of sequential and random lysine–phenylalanine copolypeptides

The sequential copolypeptides (Lys-Phe-Lys)_n and (Lys₂-Phe-Lys)_n and a series of related random copolypeptides were investigated with respect of their ability to adopt the α-helix or β-conformation. Conformational transitions were induced by increasing the pH or by addition of NaClO₄ or methanol and were observed by recording the CD spectra. In contrast to the respective alternating copolypeptide (Phe-Lys)_n with its strong tendency for the β-structure reported previously, (Lys-Phe-Lys)_n can adopt either secondary structure, whereas (Lys₂-Phe-Lys)_n strongly favors the α-helix. Together with the random copolypeptides, whose composition varied from 20 to 50 mol % phenylalanine and whose average molecular weights ranged from 10,000 to 90,000, the influence of the phenylalanine content and of the chain length on conformational stability and the rotatory strength of the respective secondary structures were elaborated.     

Functional morphological analysis of evolution of ribbing in pliocene viviparid shells from Croatia

Posilović, H., & Bajraktarević, Z. 2010: Functional morphological analysis of evolution of ribbing in pliocene viviparid shells from Croatia. Lethaia, 10.1111/j.1502‐3931.2009.00209.x. This paper provides a functional analysis of Pliocene freshwater gastropods from the phylogenetic lineage of Viviparus neumayri to Viviparus ornatus. On this section of the phylogenetic line, it is possible to follow the continuous evolution of the shell ornamentation (shouldering and rib formation) from ancestral V. neumayri with smooth shell to V. ornatus with spiral ribs. The shell morphology and possible structural function of rib development is discussed from the analytical point of view, but also by Finite Element Modelling. Spiral rib development in the viviparids is not correlated with shell thickening, but rather with strengthening of the shell is achieved through development of spiral ribs, with direct biomechanical and evoloutionary significance. □Croatia, functional morphology, gastropod shell evolution, Pliocene, viviparid evolution.     

Response properties of FM-FM combination-sensitive neurons in the auditory cortex of the mustached bat

Summary For echolocation, the mustached bat,Pteronotus parnellii rubiginosus, emits orientation sounds (pulses) and listens to echoes. Each pulse is made up of 8 components, of which 4 are constant frequencies (CF_1–4) and 4 are frequency-modulated (FM_1–4). Target-range information, conveyed by the time delay of the echo FM from the pulse FM, is processed in this species by specialized neurons in a part of the auditory cortex known as the FM-FM area. These cortical neurons are responsive to pulse-echo pairs at specific echo delays (Fig. 1). The essential components in the sound pair include the pulse FM₁ followed by an echo FM_n (n=2, 3 or 4). Downward sweeping FM₁-FM_n sounds that are similar to those the animal naturally hears during echolocation are the most effective in evoking facilitative responses. Most FM-FM neurons, however, still exhibit facilitative responses to stimulus pairs consisting of upward sweeping FM sounds and/or pure tones at frequencies found in FM sweeps (Figs. 2 and 3). The magnitude of facilitation is altered by changes in echo rather than pulse amplitude (Figs. 5 and 6). Neurons characterized by shorter best delays (or echoes from closer targets) do not require larger best echo amplitudes for facilitation.Abbreviations CF constant frequency - FM frequency modulation - H _n CF — FM harmonics of the mustached bat biosonar signal - CF _n CF components of the harmonics - FM _n FM components of the harmonics - PCF _n pulse CF_n - ECF _n echo CF_n - PFM _n pulse FM_n - EFM _n echo FM_n - PH _n pulse H_n - EH _n echo H_n - BA best amplitude for facilitation - BD best delay for facilitation - PST peri-stimulus-time - PSTC peri-stimulus-time-cumulative - dB SPL dB re 20 Pa     

Diatom life cycles and ecology in the Cretaceous

The earliest known diatom fossils with well‐preserved siliceous frustules are from Lower Cretaceous neritic marine deposits in Antarctica. In this study, we analyzed the cell wall structure to establish whether their cell and life cycles were similar to modern forms. At least two filamentous species (Basilicostephanus ornatus and Archepyrgus melosiroides) had girdle band structures that functioned during cell division in a similar way to present day Aulacoseira species. Also, size analyses of cell diameter indicated that the cyclic process of size decline and size restoration used to time modern diatom life cycles was present in five species from the Lower Cretaceous (B. ornatus, A. melosiroides, Gladius antiquus, Ancylopyrgus reticulatus, Kreagra forfex) as well as two species from Upper Cretaceous deposits (Trinacria anissimowii and Eunotogramma fueloepi) from the Southwest Pacific. The results indicate that the “Diatom Sex Clock” was present from an early evolutionary stage. Other ecological adaptations included changes in mantle height and coiling. Overall, the results suggest that at least some of the species in these early assemblages are on a direct ancestral line to modern forms.