Purification of synchronized E. coli transcription elongation complexes by reversible immobilization on magnetic beads

Synchronized transcription elongation complexes (TECs) are a fundamental tool for in vitro studies of transcription and RNA folding. Transcription elongation can be synchronized by omitting one or more NTPs from an in vitro transcription reaction so that RNA polymerase can only transcribe to the first occurrence of the omitted nucleotide(s) in the coding DNA strand. This approach was developed over four decades ago and has been applied extensively in biochemical investigations of RNA polymerase enzymes, but has not been optimized for RNA-centric assays. In this work, we describe the development of a system for isolating synchronized TECs from an in vitro transcription reaction. Our approach uses a custom 5′ leader sequence, called C3-SC1, to reversibly capture synchronized TECs on magnetic beads. We first show that complexes isolated by this procedure, called C3-SC1TECs, are >95% pure, >98% active, highly synchronous (94% of complexes chase in <15s upon addition of saturating NTPs), and compatible with solid-phase transcription; the yield of this purification is ~8%. We then show that C3-SC1TECs perturb, but do not interfere with, the function of ZTP-sensing and ppGpp-sensing transcriptional riboswitches. For both riboswitches, transcription using C3-SC1TECs improved the efficiency of transcription termination in the absence of ligand but did not inhibit ligand-induced transcription antitermination. Given these properties, C3-SC1TECs will likely be useful for developing biochemical and biophysical RNA assays that require high-performance, quantitative bacterial in vitro transcription.

The first xiphydriid wood wasp in Cretaceous amber (Hymenoptera: Xiphydriidae) and a potential association with Cycadales

A new genus and species of fossil wood wasp is described and figured from mid-Cretaceous Kachin amber, representing the first occurrence of the family Xiphydriidae in the fossil record. Paraxiphydria resinata gen. et sp. nov. exhibits typical apomorphies of the family including a generally cylindrical body, elongate neck and dome-shaped head. Nonetheless, owing to a unique combination of traits including features hitherto unknown among species of the family, the genus is classified within a separate subfamily, Paraxiphydriinae subfam. nov. A key is presented to the suprageneric groups of Xiphydriidae. The newly described species is the first fossil xiphydriid wood wasp, extends the occurrence of Xiphydriidae into the mid-Cretaceous and adds to the known diversity of features in the family. Lastly, the simplification of wing venation and hypotheses of host-plant affiliations of early xiphydriids are discussed. We evaluate pollen associated with the wasp, assign it to the genus Cycadopites and conclude that an affiliation to the Cycadales is most likely. Article and nomenclatural acts are registered in ZooBank (http://zoobank.org/, last access: 15 December 2021), with the following life science identifier (LSID) (reference): urn:lsid:zoobank.org:pub:DA80920E-E94B-4A8E-A817-077FA7BD7D69.

Fossil Leaves of Meliosma (Sabiaceae) With Associated Pollen and a Eupodid Mite From the Eocene of Maoming Basin, South China

A first occurrence of the genus Meliosma (Sabiaceae) is reported from the upper Eocene of the Maoming Basin of South China. This fossil is one of the oldest reliable records of the genus within its modern center of diversity. Fossil leaves are assigned to a new species, Meliosma eosinica sp. nov. based on leaf morphology and epidermal characters. The leaf epidermal anatomy of fossil Meliosma is illustrated for the first time. We also provide the first SEM observation of pollen grains associated with Meliosma. This study also documents an occurrence of mites within the leaf domatia previously unknown from the fossil record. We presume that the studied mite belongs to the superfamily Eupodoidea (Arthropoda), and probably the family Eupodidae, which comprises very small soft-bodied cosmopolitan mites occupying a wide range of terrestrial habitats. Additionally, we analyze the damage types on the fossil leaves of Meliosma. They exhibit exclusively external foliage feeding damage caused by arthropods and traces of probable fungal infection. A review of currently known fossil occurrences of leaves, fruits, and wood of Meliosma provides evidence for the geological and geographical distribution of the genus.

Gastrointestinal parasites in captive and free-living wild birds in Goiania Zoo

Helminths are endoparasites that infect a variety of bird species. Endoparasite infections can cause severe diseases, including kill captive avian hosts and represents a problem to maintenance and conservation. The eggs and larval forms of these parasites are usually eliminated in the host feces. The main interest of this study is to report the occurrence of eggs and oocysts in feces from captive wild birds in Goiânia Zoo and free-living birds in its surroundings. The fecal samples were subjected to parasitological examination to identify the presence of helminths and to classify their eggs based on morphological characteristics. Eggs of nematode parasites (Positive/N) were identified as Ascaridia spp. in Brotogeris chiriri (2/2), Dromaius novaehollandiae (1/1) and Rhea americana (2/2); Ascarididae in Pavo cristatus nigripensis (1/1); Capillaria spp. in Ara chloropterus (1/1) and Penelope jacucaca (1/1); Capillaria plagiaticia in Anodorhynchus hyacinthinus (1/2) and Ara spp. (2/2); Capillaria venusta in Rhamphastus tucanus (1/2); and unidentified nematode eggs from Amazona amazonica (2/2). Eimeria spp. oocyst was founded in feces from A. hyacinthinus (1/2). Considering free-living birds, Diphyllobothrium spp. eggs were founded in Ardea alba (2/2) and Nycticorax nycticorax (2/3). Co-infection of Eustrongylides spp. was founded in A. alba (1/2). This is the first occurrence of: Ascaridia spp. parasitizing B. chiriri; and C. venusta parasitizing R. tucanus. In conclusion, the helminth eggs found in the abovementioned host bird species are consistent with those reported in the literature, and treatment and control protocols were based on their identification.

Grapevine defoliation by Spodoptera frugiperda Smith, 1797 (Lepidoptera: Noctuidae) in Brazil

ABSTRACT: The fall armyworm, Spodoptera frugiperda Smith, 1797 (Lepidoptera: Noctuidae), is a polyphagous pest that causes losses in several crops. The knowledge of host plants is essential for establishing management and control strategies. The present study reported the first occurrence of S. frugiperda in Brazilian grapevines. It is recommended that further studies should be carried out in the laboratory to understand the biological aspects of the damage to different structures (leaves and grapes). This information will be essential to assess the potential of S. frugiperda damage to vines.

Deaf and Hard-of-hearing Users Evaluating Designs for Highlighting Key Words in Educational Lecture Videos

There are style guidelines for authors who highlight important words in static text, e.g., bolded words in student textbooks, yet little research has investigated highlighting in dynamic texts, e.g., captions during educational videos for Deaf or Hard of Hearing (DHH) users. In our experimental study, DHH participants subjectively compared design parameters for caption highlighting, including: decoration (underlining vs. italicizing vs. boldfacing), granularity (sentence level vs. word level), and whether to highlight only the first occurrence of a repeating keyword. In partial contrast to recommendations in prior research, which had not been based on experimental studies with DHH users, we found that DHH participants preferred boldface, word-level highlighting in captions. Our empirical results provide guidance for the design of keyword highlighting during captioned videos for DHH users, especially in educational video genres.

West Nile Virus Lineage 1 in Italy: Newly Introduced or a Re-Occurrence of a Previously Circulating Strain?

In Italy, West Nile virus (WNV) appeared for the first time in the Tuscany region in 1998. After 10 years of absence, it re-appeared in the areas surrounding the Po River delta, affecting eight provinces in three regions. Thereafter, WNV epidemics caused by genetically divergent isolates have been documented every year in the country. Since 2018, only WNV Lineage 2 has been reported in the Italian territory. In October 2020, WNV Lineage 1 (WNV-L1) re-emerged in Italy, in the Campania region. This is the first occurrence of WNV-L1 detection in the Italian territory since 2017. WNV was detected in the internal organs of a goshawk (Accipiter gentilis) and a kestrel (Falco tinnunculus). The RNA extracted in the goshawk tissue samples was sequenced, and a Bayesian phylogenetic analysis was performed by a maximum-likelihood tree. Genome analysis, conducted on the goshawk WNV complete genome sequence, indicates that the strain belongs to the WNV-L1 Western-Mediterranean (WMed) cluster. Moreover, a close phylogenetic similarity is observed between the goshawk strain, the 2008–2011 group of Italian sequences, and European strains belonging to the Wmed cluster. Our results evidence the possibility of both a new re-introduction or unnoticed silent circulation in Italy, and the strong importance of keeping the WNV surveillance system in the Italian territory active.

New records of Leptoglossus occidentalis Heidemann (Hemiptera: Coreidae) in Argentine Patagonia

New records of Leptoglossus occidentalis Heidemann from Andean region is given, becoming the first occurrence within the province of Chubut. The specimens were collected in different environments of urban and periurban areas -both domiciliary and peridomiciliary-, from Esquel, Trevelin and Aldea Escolar. This report extends its southern distribution area to the parallel 43°S.

Improvement of Performance for Raman Assisted BOTDR by Analyzing Brillouin Gain Spectrum

We propose a simplified partitioned Brillouin gain spectrum (BGS) analysis method to enhance the spatial resolution and measurement accuracy of a Brillouin optical time-domain reflectometer (BOTDR) assisted by a first-order Raman pump. We theoretically derive the mathematical model of the partitioned BGS and analyze the superposition process of sub-Brillouin signals within a theoretical spatial resolution range. We unified all the unknown constant parameters of the calculation process to simplify the partitioned BGS analysis method and the value of the uniform parameter is attained through the system test data and numerical analysis. Moreover, to automate data processing, the starting point of the temperature/strain change is determined by the first occurrence of the maximum Brillouin frequency shift (BFS), then the position where the partitioned BGS analysis method calculation begins is obtained. Using a 100 ns probe pulse and partitioned BGS analysis method, we obtain a spatial resolution of 0.4 m in the 78.45-km-long Raman-assisted BOTDR system, and the measurement accuracy is significantly improved. In addition, we achieve a strain accuracy of 5.6 με and a spatial resolution of 0.4 m in the 28.5-km-long BOTDR without Raman amplification.

Contributing to the knowledge of Brazilian Sphingidae diversity: the first record of Adhemarius daphne daphne Boisduval, 1785 and Amphimoea walkeri Boisduval, 1785 in South Brazil

Three individuals (two males and one female) of Adhemarius daphne daphne Boisduval, 1785 and an exemplar of Amphimoea walkeri Boisduval, 1785, were caught in Maquiné and Cerro Largo municipalities, respectively, indicating the first occurrence of these two taxa in the Rio Grande do Sul state, South Brazil.