Cryoseston in Stara Planina (Balkan) Mountains, Bulgaria

Numerous snow fields persisted in the Stara Planina (Central Balkan) Mountains, some with a very light tint, but with dirty surfaces, at the end of May 2009. The cryoseston community was quite different in individual snow fields. We found Chlorophyta: zygospores of Chloromonas nivalis and Chloromonas rostafiñski, Chromophyta: Chromulina elegans, Bacillariophyceae: Aulacoseira granulata var. angustissima, Aulacoseira italica, Cyclotella menenghiniana, Navicula nivalis, Hantzschia amphioxys, Fungi: Chionaster nivalis and Selenotila nivalis. Alpine species such as Chlamydomonas nivalis were not found in the snow fields studied, even though they were located in the alpine zone

Cryoseston of the Pirin Mountains, Bulgaria

In the cryoseston community of the Pirin Mountains, 18 species were determined. Chlorophyta: Chlamydomonas nivalis (predominant), Chloromonas brevispina,Chloromonas rostafinski, Chlainomonas rubra (new genus and species for Bulgaria, documented in Europe for only the second time), Cystococcus nivicolus and Stichococcus nivalis. Bacillariophyceae: Aulacoseira granulata var. angustissima, Hantzchia amphioxys, cf. Surirella. Fungi: cf. Chytridium chlamydococcii. Deuteromycetes: Selenotila nivalis, Chionaster nivalis, and saprophytic fungae cf. Myzocytium, Rhodosporidium toruloides, Alternaria sp. and cf. Cladosporium, in pollen grains. Bacteria: Leptothrixochracea. Ciliata: Vorticella campanula. The composition of cryoseston in the Pirin Mountains is characteristic for high mountains where Chlamydomonas nivalis predominates

Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites

The translational activity of the hepatitis C virus (HCV) internal ribosome entry site (IRES) and other HCV-like IRES RNAs depends on structured RNA elements in domains II and III, which serve to recruit the ribosomal 40S subunit, eukaryotic initiation factor (eIF) 3 and the ternary eIF2/Met-tRNAiMet/GTP complex and subsequently domain II assists subunit joining. Porcine teschovirus-1 talfan (PTV-1) is a member of the Picornaviridae family, with a predicted HCV-like secondary structure, but only stem-loops IIId and IIIe in the 40S-binding domain display significant sequence conservation with the HCV IRES. Here, we use chemical probing to show that interaction sites with the 40S subunit and eIF3 are conserved between HCV and HCV-like IRESs. In addition, we reveal the functional role of a strictly conserved co-variation between a purine–purine mismatch near the pseudoknot (A–A/G) and the loop sequence of domain IIIe (GAU/CA). These nucleotides are involved in a tertiary interaction, which serves to stabilize the pseudoknot structure and correlates with translational efficiency in both the PTV-1 and HCV IRES. Our data demonstrate conservation of functional domains in HCV and HCV-like IRESs including a more complex structure surrounding the pseudoknot than previously assumed

Influence of Hide Thickness on the Ability to Predict Percent Intramuscular Fat with Real-time Ultrasound in Beef Cattle

Seven hundred forty (740) head of cattle were scanned with real-time ultrasound. Models developed by Iowa State University were used to predict percent intramuscular fat on these cattle. Hide thickness was also measured on each animal and the relationship between hide thickness and accuracy of predicting percent intramuscular fat with ultrasound was evaluated. Overall, hide thickness has little effect on accuracy of ultrasound to predict percent intramuscular fat. However some particular groups (i.e. thick hided cattle scanned with Aloka technology) may be prone to underestimation of percent intramuscular fat with ultrasound

Congruency effect between articulation and grasping in native English speakers

Previous studies have shown congruency effects between specific speech articulations and manual grasping actions. For example, uttering the syllable [kɑ] facilitates power grip responses in terms of reaction time and response accuracy. A similar association of the syllable [ti] with precision grip has also been observed. As these congruency effects have been to date shown only for Finnish native speakers, this study explored whether the congruency effects generalize to native speakers of another language. The original experiments were therefore replicated with English participants (N=16). Several previous findings were reproduced, namely the association of syllables [kɑ] and [ke] with power grip and of [ti] and [te] with precision grip. However, the association of vowels [ɑ] and [i] with power and precision grip, respectively, previously found for Finnish participants, was not significant for English speakers. This difference could be related to ambiguities of English orthography and pronunciation variations. It is possible that for English speakers seeing a certain written vowel activates several different phonological representations associated with that letter. If the congruency effects are based on interactions between specific phonological representations and grasp actions, this ambiguity might lead to weakening of the effects in the manner demonstrated here

Connections of Grasping and Horizontal Hand Movements with Articulation in Czech Speakers

We have recently shown in Finnish speakers that articulation of certain vowels and consonants has a systematic influence on simultaneous grasp actions as well as on forward and backward hand movements. Here we studied whether these effects generalize to another language, namely Czech. We reasoned that if the results generalized to another language environment, it would suggest that the effects arise through other processes than language-dependent semantic associations. Rather, the effects would be likely to arise through language-independent interactions between processes that plan articulatory gestures and hand movements. Participants were presented with visual stimuli specifying articulations to be uttered (e.g., A or I), and they were required to produce a manual response concurrently with the articulation. In Experiment 1 they responded with a precision or a power grip, whereas in Experiment 2 they responded with a forward or a backward hand movement. The grip congruency effect was fully replicated: the consonant [k] and the vowel [alpha] were associated with power grip responses, while the consonant [t] and the vowel [i] were associated with precision grip responses. The forward/backward congruency effect was replicated with vowels [alpha], [o], which were associated with backward movement and with [ i], which was associated with forward movement, but not with consonants [k] and [ t]. These findings suggest that the congruency effects mostly reflect interaction between processes that plan articulatory gestures and hand movements with an exception that the forward/backward congruency effect might only work with vowel articulation.Peer reviewe

Strategy for automated NMR resonance assignment of RNA: application to 48-nucleotide K10

A procedure is presented for automated sequence-specific assignment of NMR resonances of uniformly [13C, 15N]-labeled RNA. The method is based on a suite of four through-bond and two through-space high-dimensional automated projection spectroscopy (APSY) experiments. The approach is exemplified with a 0.3mM sample of an RNA stem-loop with 48 nucleotides, K10, which is responsible for dynein-mediated localization of Drosophila fs(1)K10 mRNA transcripts. The automated analysis of the APSY data led to highly accurate and precise 3- to 4-dimensional peak lists. They provided a reliable basis for the subsequent sequence-specific resonance assignment with the algorithm FLYA and resulted in the fully automated resonance assignment of more than 80% of the resonances of the 13C-1H moieties at the 1′, 2′, 5, 6, and 8 positions in the nucleotides. The procedure was robust with respect to numerous impurity peaks, low concentration of this for NMR comparably large RNA, and structural features such as a loop, single-nucleotide bulges and a non-Watson-Crick wobble base pairs. Currently, there is no precise chemical shift statistics (as used by FLYA) for RNA regions which deviate from the regular A-form helical structure. Reliable and precise peak lists are thus required for automated sequence-specific assignment, as provided by APSY

Physicochemical analysis of rotavirus segment 11 supports a 'modified panhandle' structure and not the predicted alternative tRNA-like structure (TRLS)

.Rotaviruses are a major cause of acute gastroenteritis, which is often fatal in infants. The viral genome consists of 11 double-stranded RNA segments, but little is known about their cis-acting sequences and structural elements. Covariation studies and phylogenetic analysis exploring the potential structure of RNA11 of rotaviruses suggested that, besides the previously predicted "modified panhandle" structure, the 5' and 3' termini of one of the isoforms of the bovine rotavirus UKtc strain may interact to form a tRNA-like structure (TRLS). Such TRLSs have been identified in RNAs of plant viruses, where they are important for enhancing replication and packaging. However, using tRNA mimicry assays (in vitro aminoacylation and 3'- adenylation), we found no biochemical evidence for tRNA-like functions of RNA11. Capping, synthetic 3' adenylation and manipulation of divalent cation concentrations did not change this finding. NMR studies on a 5'- and 3'-deletion construct of RNA11 containing the putative intra-strand complementary sequences supported a predominant panhandle structure and did not conform to a cloverleaf fold despite the strong evidence for a predicted structure in this conserved region of the viral RNA. Additional viral or cellular factors may be needed to stabilise it into a form with tRNA-like properties

Mechanical unfolding of RNA: From hairpins to structures with internal multiloops

Mechanical unfolding of RNA structures, ranging from hairpins to ribozymes, using laser optical tweezer (LOT) experiments have begun to reveal the features of the energy landscape that cannot be easily explored using conventional experiments. Upon application of constant force ($f$), RNA hairpins undergo cooperative transitions from folded to unfolded states whereas subdomains of ribozymes unravel one at a time. Here, we use a self-organized polymer (SOP) model and Brownian dynamics simulations to probe mechanical unfolding at constant force and constant-loading rate of four RNA structures of varying complexity. Our work shows (i) the response of RNA to force is largely determined by the native structure; (ii) only by probing mechanical unfolding over a wide range of forces can the underlying energy landscape be fully explored.Comment: 26 pages, 6 figures, Biophys. J. (in press

Multiple segmental and selective isotope labeling of large RNA for NMR structural studies

Multiple segmental and selective isotope labeling of RNA with three segments has been demonstrated by introducing an RNA segment, selectively labeled with 13C9/15N2/2H(1′, 3′, 4′, 5′, 5′′)-labeled uridine residues, into the central position of the 20 kDa ε-RNA of Duck Hepatitis B Virus. The RNA molecules were produced via two efficient protocols: a two-step protocol, which uses T4 DNA ligase and T4 RNA ligase 1, and a one-pot protocol, which uses T4 RNA ligase 1 alone. With T4 RNA ligase 1 all not-to-be-ligated termini are usually protected to prevent formation of side products. We show that such labor-intensive protection of termini is not required, provided segmentation sites can be chosen such that the segments fold into the target structure or target-like structures and thus are not trapped into stable alternate structures. These sites can be reliably predicted via DINAMelt. The simplified NMR spectrum provided evidence for the presence of a U28 H3-imino resonance, previously obscured in the fully labeled sample, and thus of the non-canonical base pair U28:C37. The demonstrated multiple segmental labeling protocols are generally applicable to large RNA molecules and can be extended to more than three segments