An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3′-untranslated region

Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.

Quantification and evolution of mitochondrial genome rearrangement in Amphibians

Background Rearrangement is an important topic in the research of amphibian mitochondrial genomes ("mitogenomes" hereafter), whose causes and mechanisms remain enigmatic. Globally examining mitogenome rearrangements and uncovering their characteristics can contribute to a better understanding of mitogenome evolution. Results Here we systematically investigated mitogenome arrangements of 232 amphibians including four newly sequenced Dicroglossidae mitogenomes. The results showed that our new sequenced mitogenomes all possessed a trnM tandem duplication, which was not exclusive to Dicroglossidae. By merging the same arrangements, the mitogenomes of ~ 80% species belonged to the four major patterns, the major two of which were typical vertebrate arrangement and typical neobatrachian arrangement. Using qMGR for calculating rearrangement frequency (RF) (%), we found that the control region (CR) (RF = 45.04) and trnL2 (RF = 38.79) were the two most frequently rearranged components. Forty-seven point eight percentage of amphibians possessed rearranged mitogenomes including all neobatrachians and their distribution was significantly clustered in the phylogenetic trees (p < 0.001). In addition, we argued that the typical neobatrachian arrangement may have appeared in the Late Jurassic according to possible occurrence time estimation. Conclusion It was the first global census of amphibian mitogenome arrangements from the perspective of quantity statistics, which helped us to systematically understand the type, distribution, frequency and phylogenetic characteristics of these rearrangements.

An African Tick Flavivirus Forming an Independent Clade Exhibits Unique Exoribonuclease-Resistant RNA Structures in the Genomic 3′-Untranslated Region

Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa is limited. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts leading to significant public health problems. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibits unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.

Comparisons of N-glycans across invertebrate phyla

Many invertebrates are either parasites themselves or vectors involved in parasite transmission; thereby, the interactions of parasites with final or intermediate hosts are often mediated by glycans. Therefore, it is of interest to compare the glycan structures or motifs present across invertebrate species. While a typical vertebrate modification such as sialic acid is rare in lower animals, antennal and core modifications of N-glycans are highly varied and range from core fucose, galactosylated fucose, fucosylated galactose, methyl groups, glucuronic acid and sulphate through to addition of zwitterionic moieties (phosphorylcholine, phosphoethanolamine and aminoethylphosphonate). Only in some cases are the enzymatic bases and the biological function of these modifications known. We are indeed still in the phase of discovering invertebrate glycomes primarily using mass spectrometry, but molecular biology and microarraying techniques are complementary to the determination of novel glycan structures and their functions.

Patterns of aquatic decay and disarticulation in juvenile Indo-Pacific crocodiles (Crocodylus porosus), and implications for the taphonomic interpretation of fossil crocodyliform material

High levels of skeletal articulation and completeness in fossil crocodyliforms are commonly attributed to rapid burial, with decreasing articulation and completeness thought to result from prolonged decay of soft tissue and the loss of skeletal connectivity during ‘bloat and float’. These interpretations are based largely on patterns of decay in modern mammalian and avian dinosaur carcasses. To address this issue, we assessed the decay of buried and unburied juvenile Crocodylus porosuscarcasses in a controlled freshwater setting. The carcasses progressed through typical vertebrate decay stages (fresh, bloated, active decay, and advanced decay), reaching the final skeletal stage on average 56 days after death. Unburied carcasses commenced floating five days post-mortem during the bloated stage, and one buried carcass only commenced floating 12 days post-mortem. While floating, skeletal elements remained articulated within the still coherent dermis, except for thoracic ribs, ischia and pubic bones. The majority of disarticulation occurred at the sediment-–water interface after the carcasses sank during the advanced decay stage, ~ 36 days post-mortem. Based on these results we conclude that fossil crocodyliform specimens displaying high levels of articulation are not the result of prolonged subaerial and subaqueous decay in a low-energy, aqueous environment. Using extant juvenile C. porosus as a proxy for fossil crocodyliforms, rapid burial in an aquatic setting would have to occur prior to the carcass floating, and would also have to continually negate the positive buoyancy associated with bloating. Rapid burial does not have to be the only avenue to preservation of articulation, as other mechanisms such as physical barriers and internal physiological chemistry could prevent carcasses from floating and subsequently disarticulating upon sinking. The inference that a large proportion of skeletal elements could drift from floating carcasses in a low energy setting with minimal scavenging, thereby causing a loss of completeness, seems unlikely.

The complete mitochondrial genomes of nine white-tailed deer subspecies and their genomic differences

The white-tailed deer ( Odocoileus virginianus ) is an important, sustainable-use species in Mexico; 14 subspecies are widely distributed throughout the Mexican territory. The criteria for classifying subspecies is based on morphological features throughout their geographical range; however, the complete genetic characterization of Mexican subspecies has not been established. The objective of the present work is to report the mitogenomes of 9 of the 14 white-tailed deer subspecies from Mexico and identify their unique variations. Typical vertebrate mitogenomes structures (i.e., 13 protein-coding genes, 22 tRNA genes, and 2 rRNA genes) were observed in the studied subspecies. The greatest numbers of polymorphisms were identified in the D-loop, ND4, ND5, CYTB/COI, ATP6, and COIII genes. Phylogenetic analyses showed that the southern and southeastern subspecies were distinct from the central and northern subspecies; the greatest genetic distances were also observed between these 2 groups. These subspecies-specific variations could be useful for designing a strategy to genetically characterize the studied subspecies. El venado cola blanca es una de las especies de mayor importancia dentro del aprovechamiento de la fauna silvestre de México, donde se distribuyen de manera natural 14 subespecies. Actualmente, estas subespecies se han clasificado de acuerdo a sus variaciones fenotípicas que presentan a lo largo de su rango de distribución, sin embargo no se ha establecido la caracterización genética completa de las mismas. Es por esto que el objetivo del presente estudio es reportar los mitogenomas de 9 de las 14 subespecies de venado cola blanca, así como identificar las variaciones únicas de cada subespecie. En las 9 subespecies se observó la estructura típica de los mitogenomas de vertebrados (13 genes que codifican para proteínas, 22 ARNt, 2 ARNr). Los genes con mayor polimorfismo fueron D-loop, ND4, ND5, CYTB/COI, ATP6 y COIII. El análisis filogenético mostró la separación de las subespecies del sur y sureste de las subespecies del centro y norte del país, a su vez las distancias genéticas entre estos dos grupos fueron las más altas. Estas variaciones subespecie-específicas podrían ser útiles para diseñar una estrategia para caracterizar genéticamente las subespecies estudiadas.

The first complete mitochondrial genome of Pygopodidae (Aprasia parapulchella Kluge)

The Pygopodidae comprise an enigmatic group of legless lizards endemic to the Australo-Papuan region. Here we present the first complete mitochondrial genome for a member of this family, Aprasia parapulchella, from Australia. The mitochondrial genome of A. parapulchella is 16 528 base pairs long and contains 13 protein-coding genes, 22 tRNA genes, two rRNA genes and the control region, conforming to the typical vertebrate gene order. The overall mitochondrial nucleotide composition is 31.7% A, 24.5% T, 30.5% C and 13.2% G. This corresponds to a total A+T content of 56.3%, which is similar to that of other squamate lizard genomes.

The complete mitochondrial DNA genome of Eremias brenchleyi (Reptilia: Lacertidae) and its phylogeny position within squamata reptiles

Squamata is the most diversified reptilian order that has been traditionally classified into three suborders – Lacertilia, Serpentes and Amphisbaenia in which Lacertilia have about 16-19 families. But the phylogenetic relationships among major groups of Lacertilia remain controversial. In this paper, the complete mitochondrial DNA sequence of Eremias brenchleyi was determined by using long-and-accurate PCR (LA-PCR). The mtDNA sequence is 19 542 bp, making it the longest mitochondrial genome in squamates species reported so far. It shows the typical vertebrate arrangement of genes. The control region of E. brenchleyi was characterized by two conspicuous 65 bp and 56 bp tandem repeats at its 5′ and 3′ terminus respectively. In order to study the higher level relationships of squamates, the phylogenetic study including all currently available squamates mitochondrial sequences was carried out. We obtained a relationship of 16 families of lizards (Lacertidae, Scincidae, Iguanidae, Chameleonidae, Agamidae, Trogonophidae, Bipedidae, Shinisauridae, Helodermatidae, Amphisbaenidae, Gekkonidae, Varanidae, Anguidae, Xantusiidae, Rhineuridae, Cordylidae) and 8 families of Serpentes. The internal relationships within this group yielded high bootstrap support and were more congruent with morphological analyses.

Dynamics of Transitional Endoplasmic Reticulum Sites in Vertebrate Cells

A typical vertebrate cell contains several hundred sites of transitional ER (tER). Presumably, tER sites generate elements of the ER–Golgi intermediate compartment (ERGIC), and ERGIC elements then generate Golgi cisternae. Therefore, characterizing the mechanisms that influence tER distribution may shed light on the dynamic behavior of the Golgi. We explored the properties of tER sites using Sec13 as a marker protein. Fluorescence microscopy confirmed that tER sites are long-lived ER subdomains. tER sites proliferate during interphase but lose Sec13 during mitosis. Unlike ERGIC elements, tER sites move very little. Nevertheless, when microtubules are depolymerized with nocodazole, tER sites redistribute rapidly to form clusters next to Golgi structures. Hence, tER sites have the unusual property of being immobile, yet dynamic. These findings can be explained by a model in which new tER sites are created by retrograde membrane traffic from the Golgi. We propose that the tER–Golgi system is organized by mutual feedback between these two compartments.