Identification, bioinformatic analysis and expression profiling of candidate mRNA-like non-coding RNAs in Sus scrofa

Messenger RNA-like non-coding RNAs （mlncRNAs） are a newly identified group of non-coding RNAs （ncRNAs） that may be involved in a number of critical cellular events. In this study, 93 candidate porcine mlncRNAs were obtained by computational prediction and screening, among which 72 were mapped to the porcine genome. Further analysis of 8 representative candidates revealed that these mlncRNA candidates are not highly conserved among species. Remarkably, one of the candidates, sTF35495, was found to be precursor of a putative porcine microRNA. By RACE PCR, we determined that the full length of sTF35495 was 3 kb. The protein-coding potential of this RNA was tested in silico with no significant finding. Semi-quantitative RT-PCR analysis of the subgroup of 8 candidates revealed two distinct expression profiles and two molecules were further validated by real-time PCR. The predicted pre-microRNA sequence in this study provides a potentially interesting insight into the in vivo function of porcine mlncRNAs and our findings suggest that they play key biological roles in Sus scrofa.     

The Earliest Normal Flower from Liaoning Province,China

The early evolution of angiosperms has been a focus of intensive research for more than a century. The Yixian Formation in western Liaoning yields one of the earliest angiosperm macrofioras. Despite multitudes of angiosperm fossils uncovered, including Archaefructus and Sinocarpus, no bona fide normal flower has been dated to 125 Ma （mega-annum） or older. Here we report Callianthus dilae gen. et sp. nov. from the Yixian Formation （Early Cretaceous） in western Liaoning, China as the earliest normal flower known to date. The flower demonstrates a typical floral organization, including tepals, androecium, and gynoecium. The tepals are spatulate with parallel veins. The stamens have a slender filament, a globular anther, bristles at the anther apex, and in situ round-triangular pollen grains. The gynoecium is composed of two stylate carpels enclosed in a fleshy envelope, and develops into a ＂hip＂ when mature. Since the well-accepted history of angiosperms is not much longer than 125 Ma, Callianthus together with Chaoyangia, Archaefructus and Sinocarpus from the Yixian Formation demonstrate a surprisingly high diversity of angiosperms, implying a history of angiosperms much longer than currently accepted.     

The influence of terrain age and altitude on the arthropod communities found on recently deglaciated terrain

Climate warming has been more pronounced in the Arctic than elsewhere, resulting in a recent rapid glacial retreat. Over 85% of the Almajallojekna glacier has disappeared over the last 115 years and it is one of the fastest retreating glaciers in Sweden. In 2011 and 2012, at 18 sites in the vicinity of the remaining glacier network, we sampled arthropods and related the species richness, abundance and proportion of herbivores to altitude （ranging from 824 to 1,524 m.a.s.1.） and the age of the site （ranging from 0 to 〉 115 years）. Temperature was measured at six sites and the average annual air temperature ranged from -3.7℃ to 1.1℃. In total, we recorded 3,705 arthropods from 117 species in nine different taxonomic groups. The most abundant and species-rich group was Coleoptera （1,381 individuals, 41 species） followed by Araneae （1,050 individuals, 15 species） and Macrolepidoptera （732 individuals, 17 species）. Only at lower altitudes did the abundance and species richness of arthropods increase with increasing age of the site. The results were consistent among the studied taxonomic groups and when controlling for sam- piing intensity using two different approaches. The proportion of herbivores decreased with increasing age of the site and with increasing altitude. Clearly, altitude appears more important than the age of the site and, at higher altitudes, abundance, species richness and herbivory are low [Current Zoology 60 （2）： 203-220, 2014].     

Experimentation of Fish Swimming Based on Tracking Locomotion Locus

There are many kinds of swimming mode in the fish world, and we investigated two of them, used by cyprinids and bulltrout. In this paper we track the locomotion locus by marks in different flow velocity from 0.2 m·s^-1 to 0.8 m·s^-1. By fit the data above we could find out the locomotion mechanism of the two kinds of fish and generate a mathematical model of fish kine- matics. The cyprinid fish has a greater oscillation period and amplitude compared with the bulltrout, and the bulltrout changes velocity mainly by controlling frequency of oscillation.     

Positive Selection of CAG Repeats of the ATXN2 Gene in Chinese Ethnic Groups

The ataxin-2 （ATXN2） gene is located on human chromo-some 12q24.1. In normal individuals, the coding region in exon 1 of this gene has fewer than 31 CAG repeats （Yu et al., 2005： Laffita-Mesa et al., 2012）. However, an abnormal expansion of CAG trinucleotide repeats results in the aggre-gation of polyglutamine （polyQ）, which causes spinocer-ebellar ataxia type 2 （SCA2） （Pulst et al., 1996）. The expanded alleles have more than 32 repeats in the affected individuals, and generally there is an inverse correlation between CAG repeat length and age of onset （Pulst et al., 1996）. SCA2 is an autosomal dominant inheritance neurodegenerative disease, whose major clinical feature is progressive cerebellar ataxia. Atrophies of the brainstem and frontal lobe have been frequently detected by magnetic resonance imaging （MRI） （Yamamoto-Watanabe et al., 2010）. This disease has the strong effect on sensory and motor control.     

Structural and Expressional Variations of the Mitochondrial Genome Conferring the Wild Abortive Type of Cytoplasmic Male Sterility in Rice

The so-called ＂wild abortive＂ （WA） type of cytoplasmic male sterility （CMS） derived from a wild rice species Oryza rufipogon has been extensively used for hybrid rice breeding. However, extensive analysis of the structure of the related mitochondrial genome has not been reported, and the CMS-associated gene（s） remain unknown. In this study, we exploited a mitochondrial genome-wide strategy to examine the structural and expressional variations in the mitochondrial genome conferring the CMS. The entire mitochondriai genomes of a CMS-WA line and two normal fertile rice lines were amplified by Long-polymerase chain reaction into tilling fragments of up to 15.2 kb. Restriction and DNA blotting analyses of these fragments revealed that structural variations occurred in several regions in the WA mitochondrial genome, as compared to those of the fertile lines. All of the amplified fragments covering the entire mitochondrial genome were used as RNA blot probes to examine the mitochondriai expression profile among the CMS-WA and fertile lines. As a result, only two mRNAs were found to be differentially expressed between the CMS-WA and the fertile lines, which were detected by a probe containing the nad5 and orf153 genes and the other having the ribosomal protein gene rpl5, respectively. These mRNAs are proposed to be the candidates for further identification and functional studies of the CMS gene.     

杂斑腹小鸮实为鬼鸮

Based on two specimens collected from Sichuan Province, Yang et al. (1989) described a new subspecies of the spotted little owl (Athene brama), the belly-mottled little owl (Athene brama poikila). This subspecies has been acknowledged by Cheng (2000). However, Cheng (2000) also mentioned that further work should be done on this subspecies. In 2001, we checked the specimen of Athene brama poikila in Ya’an, Sichuan and comparing them with the spotted little owl and the boreal owl (Aegolius funereus). The boreal owl is identifiable from its rather square facial disc, however, this character was destroyed during the facture for these two specimens of Athene brama poikila. That is the reason Yang et al.(1989) missed them with the genus Athene. The genus Aegolius is also identifiable from the genus Athene from the character on the toes, as the toes of the boreal owl are covered with thick feathers, whereas the toes of the little owl are bristled. The toes of these two specimens of Athene brama poikila are thickly feathered, corresponding to the identification of the genus Aegolius. The morphological characters and measurements of the two specimens also correspond to the boreal owl. The habitat of the two specimens was reported as conifer deciduous forest around 2 200 m to 3 100 m, which fits the habitat of the boreal owl. The distribution of the endemic Gansu subspecies of the boreal owl (A. f. beickianus) was reported at Tiantangsi, Lianhuashan in Gansu, Guinan in Qinghai and Jiuzhaigou in Sichuan in China, it was also reported at Lahul in north India, Sun et al. (2001) suggested that it is probably the boreal owl is also distributed in the conifer forest of west Sichuan and east Tibet. The new distribution point in Baoxing and Yajiang in Sichuan corresponds to this conjecture. As a conclusion, we believe that these two specimens should belong to the A. f. beickianus of the boreal owl .     

Parametric Research of Experiments on a Carangiform Robotic Fish

In this paper, a carangiform robotic fish with 4-DoF （degree of freedom） tail has been developed. The robotic fish has capability of swimming under two modes that are radio control and autonomous swimming. Experiments were conducted to investigate the influences of characteristic parameters including the frequency, the amplitude, the wave length, the phase difference and the coefficient on forward velocity. The experimental results shown that the swimming performance of the robotic fish is affected mostly by the characteristic parameters observed.     

Cloning and characterization of nanos gene in silkworm Bombyx mori

Gene nanos is a maternal posterior group gene required for normal development of abdominal segments and the germ line in Drosophila. Expression of nanos-related genes is associated with the germ line in a broad variety of other taxa. In this study, the 5＇-RACE method and the in silico cloning method are used to isolate the new nanos-like gene of Bombyx mor/and the gene obtained is analyzed with bioinformatics tools. The putative protein is expressed in Escherichia coli and the antiserum has been produced in New Zealand white rabbits. The result shows that the nanos cDNA is 1,913 bp in full length and contains a 954 bp open reading frame. The deduced protein has 317 amino acid residues, with a predicted molecular weight of 35 kDa, isoelectric point of 5.38, and contains a conserved nanos RNA binding domain. The conserved region of the deduced protein shares 73% homology with the nanos protein conserved region of Honeybee （Apis mellifera）. This gene has been registered in the GenBank under the accession number EF647589. One encoding sequence of the nanos fragment has been successfully expressed in E. coli. Western blotting analysis indicates that homemade antiserum can specifically detect nanos protein expressed in prokaryotic cells.     

The MNS16A polymorphism in the TERT gene in peri-centenarians from the Han Chinese population

MNS16A,a variable number of tandem repeats polymorphism in the TERT gene,has been suggested to regulate telomerase activity.As telomerase activity has been reported to be related to life-span,we hypothesized that this polymorphism might affect human longevity by controlling the length of the telomere.To test this hypothesis,we collected 446 unrelated pericentenarian individuals(age≥90,mean 94.45±3.45 years)and 332 normal controls(age 22-53,mean 35.0±12.0 years)from Dujiangyan,Sichuan,China.We typed the MNS16A polymorphism in both groups,and compared the allele and genotype frequencies between the peri-centenarian and control groups using the chi-squared test.There was no significant difference between the peri-centenarian and control groups.Thus,the MNS16A polymorphism in TERT might not influence human life-span,at least in the Han Chinese population studied here.     

Altered small-world,functional brain networks in patients with lower back pain

In this study, we aimed to investigate the functional network changes that occur in patients with lower back pain(LBP). We also investigated the link between LBP and the small-world properties of functional networks within the brain. Functional MRI(fMRI) was performed on 20 individuals with LBP and 17 age and gender-matched normal controls during the resting state. The severity of the pain in the individuals with LBP ranged from 5 to 8 on a 0–10 scale, with 0 indicating no pain. Network-based statistics were performed to investigate the differences between the brain networks of individuals with LBP and those of normal controls. Several small-world parameters of brain networks were calculated, including the clustering coefficient, characteristic path length, local efficiency, and global efficiency. These criteria reflect the overall network efficiency. The brain networks in the individuals with LBP due to herniation of a lumbar disc demonstrated a significantly longer characteristic path length as well as a lower clustering coefficient, global efficiency, and local efficiency compared to those in control subjects. We found that LBP patients tended to have unstable and inefficient brain networks when compared with healthy controls. In addition, LBP individuals showed significantly decreased functional connectivity in the anterior cingulate cortex, middle cingulate cortex, post cingulate cortex, inferior frontal gyrus, middle temporal gyrus, occipital gyrus, postcentral gyrus, precentral gyrus, supplementary motor area, thalamus, fusiform, caudate, and cerebellum. We believe that these regions may be involved in the pathophysiology of lower back pain.     

Molecular data suggests the ciliate Mesodinium (Protista: Ciliophora) might represent an undescribed taxon at class level

The well-known ciliate, Mesodinium Stein, 1863, is of great importance to marine microbial food webs and is related to the "red tides". However, it is possibly one of the most confusing ciliate taxa in terms of its systematic position: either the morphological or the molecular data excluded it from all the other known assemblages or groups. In the current work, the sequences of small subunit ribosomal RNA（SSU rR NA） genes for all isolates available are analysed and an examination of the secondary structure patterns of related groups is carried out. The results indicate that（1） Mesodinium invariably represents a completely separated and isolated clade positioned between two subphyla of ciliates with very deep branching, which indicates that they should be a primitive or ancestral group for the subphylum Intramacronucleata;（2） the secondary structure of the SSU r RNA of Mesodinium species is unusual in that, while the secondary structure of V4 in Mesodinium sp. has the deletions common to all litostome ciliates, it has more extensive deletions in helix E23₈ and a longer helix E23₁;（3） combining the phylogenetic and morphological information, we suggest establishing Mesodiniea cl. nov., including the order Mesodiniida Grain, 1994, belonging to the subphylum Intramacronucleata.     

我国首次记录的微型硅藻——具刺原龙骨藻和伊岛棒杆藻及对其分类地位的讨论

Protokeelia is described as a new and rare pennate diatom genus in China. Its valve includes two parts： ventral valve and dorsal valve. The ventral valve is more or less convex or concave. The raphe runs in a distinct elevated and thickened siliceous ridge. In the internal valve, beneath the raphe are fibulae or fibulae clusters which connect the ventral and dorsal valves. One species, P. spinifera Round ＆ Basson, is observed in the water samples from a mangrove forest in Sai Kung, Hong Kong, China. Its main morphological features are described in this paper along with electron microscope （EM） photos. Morphological comparisons are also made among several allied species. In addition, a newly recorded species for China, Rhopalodia iriomotensis Kobayasi, Nagumo ＆ Tanaka, is discussed here. Because several key features observed in this species resemble those of some Protokeelia species, we suggest that it may actually represent a Protokeelia species.     

Two New Species of Fire-Bellied Newts (Caudata,Salamandridae, Cynops) from Southeastern China

The fire-bellied newt genus Cynops contains ten known species distributed in China and Japan in East Asia.In this work,two new Cynops species are described,namely Cynops jiaoren sp.nov.distributed in northern Guangdong and Cynops maguae sp.nov.distributed in eastern Jiangxi.The two new species can be distinctly distinguished from their congeners by the independent phylogenetic placements and a combination of morphological characteristics.The discovery of these two new species in the Southeast Ch...     

Detection of erythrocytes in patients with Waldenstrom macroglobulinemia using atomic force microscopy

The pathological changes of erythrocytes are detected at the nanometer scale, which is important for revealing the onset of diseases and diagnosis. The aim of this study is to examine the ultrastructural changes of erythrocytes in Waldenstr6m macroglobulinemia （WM） at a nanometer scale. Blood samples were collected from two healthy volunteers, two WM patients, and three multiple myeloma （MM） patients when they were first diagnosed. The changes of morphology in the erythrocytes were studied at the nanometer level by high-resolution atomic force microscopy imaging （AFM）. Compared with the healthy controls and the MM patients, there were dramatic deformations in the overall shape and surface membrane of the erythrocytes in WM patients. Healthy, pathological WM, and MM erythrocytes could be distinguished by several morphological parameters, includ- ing the width, length, length-to-width ratio, valley, peak, peak-to-valley, and Ra. AFM is able to detect the morpho- logical differences in the red blood cells from WM patients, healthy controls, and MM patients. Therefore, the erythro- cyte morphology is an important parameter for the diagnosis of WM, which can be used to distinguish WM from MM. The changes of ultrastructure in red blood cells may provide a clue to reveal the mechanism of WM.     

Structural and mutational analysis of the interaction between the Middle-East respiratory syndrome coronavirus (MERS-CoV) papain-like protease and human ubiquitin

The papain-like protease(PL^pro) of Middle-East respiratory syndrome coronavirus（MERS-CoV） has proteolytic,deubiquitinating,and de ISGylating activities.The latter two are involved in the suppression of the antiviral innate immune response of the host cell.To contribute to an understanding of this process,we present here the X-ray crystal structure of a complex between MERS-CoV PL^pro and human ubiquitin（Ub） that is devoid of any covalent linkage between the two proteins.Five regions of the PL^pro bind to two areas of the Ub.The C-terminal five residues of Ub,RLRGG,are similar to the P5–P1 residues of the polyprotein substrates of the PL^pro and are responsible for the major part of the interaction between the two macromolecules.Through sitedirected mutagenesis,we demonstrate that conserved Asp165 and non-conserved Asp164 are important for the catalytic activities of MERS-CoV PL^pro.The enzyme appears not to be optimized for catalytic efficiency; thus,replacement of Phe269 by Tyr leads to increased peptidolytic and deubiquitinating activities.Ubiquitin binding by MERS-CoV PL^pro involves remarkable differences compared to the corresponding complex with SARS-CoV PL^pro.The structure and the mutational study help understand common and unique features of the deubiquitinating activity of MERS-CoV PL^pro.     

Hard to fly the nest： A study of body condition and plumage quality in house sparrow fledglings

Contrary to the nestling phase, the post-fledging phase has been less studied probably because it is challenging to follow the chicks after they fledge. However, this phase is crucial to consider when focusing on the life cycle of individuals because it is associated with new demands： After leaving the nest, individuals have to find their own food and cope with a new set of previously unknown stressors. In this study, we aimed at better understanding how energetically demanding the post-ftedging period is in house sparrows Passer domesticus by measuring several indices of a fledgling＇s state （body condition, fat and muscle scores and plumage quality）. If the energetic demands of the post-fledging period are greater than those of the adult life, we predicted that fledglings should be in lower condition and should have a plumage of lower quality relative to adults. Supporting this prediction, the condition and the plumage of fledglings differed dramatically from those of adults. Interestingly, this difference disappeared in autumn. Overall, our results suggest that the post-fledging period is probably one of the most energetically demanding of the life cycle in this species. Supporting this idea, the resighting probability of fledglings was lower relative to adults. However, resighting probability depends on many factors （mortality, dispersal, habitat use and behaviours） and future studies are necessary to tease apart their relative importance in determining resighting probability [Current Zoology 60 （4）： 449-459, 2014].     

Multiple factors correlating with wing malformations in the population of Parnassius apollo (Lepidoptera: Papilionidae) restituted from a low number of individuals: A mini review

The Apollo butterfly, Parnassius apollo (Linnaeus), was common in Europe over 100 years ago, but currently it is considered as near threatened. Different conservation programs have promoted the persistence of this species;however, it is still endangered. An example of such programs was the action devoted to reestablish the Apollo butterfly population in Pieniny National Park (Poland) from only 20-30 individuals which had survived till the last decade of the 20th century. This reintroduction has been successful;however, unexpected developmental problems appeared. Butterflies with deformed or reduced wings became frequent in the population living in the natural habitat, and particularly among those reared under seminatural conditions (in the same environment, but fenced by a net). Until recently, reasons for these malformations remained unknown. However, reports published during last months indicated that there are genetic, biochemical, and microbiological factors contributing to this phenomenon. In the malformed individuals, lesions in the wingless gene and dysfunctions of laccase 1 and 2 were found to be significantly more frequent than in normal insects. A large fraction of butterflies with deformed or reduced wings was devoid of the prokaryotic symbiont Wolbachia, which was present in most normal individuals. Moreover, Yersinia pseudotuberculosis (Pfeiffer) Smith and Thai, and Serratia sp., bacteria pathogenic to insects, were detected in the biological material from both normal and malformed butterflies from this population. These findings are summarized and discussed in this review, in the light of conservation of insects and restitution of their populations from a low number of individuals.