Molecular phylogeny and taxonomy of the genus Vernaya (Mammalia: Rodentia: Muridae) with the description of two new species.

The climbing mouse is a rare, small mammal listed as an endangered species on the China species red list. Molecular phylogenetic analyses and the evolutionary history of the genus remain unexplored because of the extreme difficulty in capturing individuals and their narrow distribution. Here, we collected 44 specimens, sequenced one mitochondrial and eight nuclear genes, and integrated morphological approaches to estimate phylogenetic relationships, delimit species boundaries, and explore evolutionary history. Molecular analyses and morphological results supported the validity of these four species. Here, we describe two new species, Vernaya meiguites sp. nov. and Vernaya nushanensis sp. nov., and recognize Vernaya foramena, previously considered a subspecies of Vernaya fulva, as a valid species. The estimated divergence time suggests that the climbing mouse began to diversify during the Pliocene (3.36 Ma).

Transposable Elements Shape the Genome Diversity and the Evolution of Noctuidae Species.

Noctuidae is known to have high species diversity, although the genomic diversity of Noctuidae species has yet to be studied extensively. Investigation of transposable elements (TEs) in this family can improve our understanding of the genomic diversity of Noctuidae. In this study, we annotated and characterized genome-wide TEs in ten noctuid species belonging to seven genera. With multiple annotation pipelines, we constructed a consensus sequence library containing 1038-2826 TE consensus. The genome content of TEs showed high variation in the ten Noctuidae genomes, ranging from 11.3% to 45.0%. The relatedness analysis indicated that the TE content, especially the content of LINEs and DNA transposons, is positively correlated with the genome size (r = 0.86, p-value = 0.001). We identified SINE/B2 as a lineage-specific subfamily in Trichoplusia ni, a species-specific expansion of the LTR/Gypsy subfamily in Spodoptera exigua, and a recent expansion of SINE/5S subfamily in Busseola fusca. We further revealed that of the four TE classes, only LINEs showed phylogenetic signals with high confidence. We also examined how the expansion of TEs contributed to the evolution of noctuid genomes. Moreover, we identified 56 horizontal transfer TE (HTT) events among the ten noctuid species and at least three HTT events between the nine Noctuidae species and 11 non-noctuid arthropods. One of the HTT events of a Gypsy transposon might have caused the recent expansion of the Gypsy subfamily in the S. exigua genome. By determining the TE content, dynamics, and HTT events in the Noctuidae genomes, our study emphasized that TE activities and HTT events substantially impacted the Noctuidae genome evolution.

BCM-DTI: A fragment-oriented method for drug-target interaction prediction using deep learning.

The identification of drug-target interaction (DTI) is significant in drug discovery and development, which is usually of high cost in time and money due to large amount of molecule and protein space. The application of deep learning in predicting DTI pairs can overcome these limitations through feature engineering. However, most works do the features extraction using the whole drug and target, which do not take the theoretical basis of pharmacological reaction that the interaction is closely related to some substructure of molecule and protein into consideration, thus poor in performance. On the other hand, some substructure-oriented studies only consider a single type of fragment, e.g., functional group. To address these issues, we propose an end-to-end predicting framework for drug-target interaction named BCM-DTI that takes diverse fragment types into account, including branch chain, common substructure and motif/fragments, and applies a feature learning module based on CNN to learn the synergistic effect between these fragments. We implement BCM-DTI on four public datasets, and the results show that BCM-DTI outperforms state-of-the-art approaches and requires lower training cost.

Characterization and phylogenetic analysis of the complete chloroplast genome of Saussurea sagittifolia (Asteraceae, Cardueae).

The species of Saussurea sagittifolia Y. S. Chen & S. R. Yi belongs to the family Asteraceae (Cardueae). The complete chloroplast genome of S. sagittifolia was assembled and annotated for the first time in this study. The complete chloroplast genome of S. sagittifolia was 152,535 bp, including a large single-copy (LSC) region of 83,511 bp, a small single-copy (SSC) region of 18,632 bp, and a pair of inverted repeats (IRs) of 25,196 bp. The overall GC content of the chloroplast genome was 37.7%. The chloroplast genome encoded 131 genes, including 87 protein-coding genes, 36 tRNA genes, and eight rRNA genes. Phylogenetic analysis based on complete chloroplast sequences revealed that it related closely to Saussurea medusa.

Molecular phylogeny and taxonomy of the genus Nectogale (Mammalia: Eulipotyphla: Soricidae).

The elegant water shrew, Nectogale elegans, is one of the small mammal species most adapted to a semi-aquatic lifestyle. The taxonomy of the genus Nectogale has received little attention due to difficulties in specimen collection. In this study, we sequenced one mitochondrial and eight nuclear genes to infer the phylogenetic relationship of Nectogale. Phylogenetic analyses revealed two large clades within Nectogale. One clade represented N. elegans, and the other was regarded as N. sikhimensis. The split between N. elegans and N. sikhimensis dated back to the early Pleistocene (2.15 million years ago [Ma]), which might be relevant to the Qinghai-Tibet Plateau (QTP) uplift. The morphological comparison showed several distinguishing characters within Nectogale: the shape of the mastoids, the first lower unicuspid (a1), and the second upper molar (M2). Overall, the molecular and the morphological evidences supported that the genus Nectogale consists of two valid species: N. elegans and N. sikhimensis.

The complete mitochondrial genome of Indian Cuckoo Cuculus micropterus (Aves: Cuculiformes).

The Indian Cuckoo, Cuculus micropterus, belongs to the family Cuculidae. In this paper, we sequenced and analysized the complete mitochondrial genome of C. micropterus. The complete mitochondrial genome of C. micropterus is 17,541 bp in length, which was submitted to the NCBI database under the accession number MZ048030. It contains 13 protein-coding genes, 22 transfer RNA genes, two ribosome RNA genes, and one non-coding control region. The overall base composition of the mitochondrial DNA is 33.2% for A, 24.2% for T, 29.8% for C, and 12.8% for G, with a GC content of 42.6%. In order to explore the molecular phylogenetics evolution of Cuculidae, the nucleotide sequence data of 13 PCGs of C. micropterus and other 11 Cuculiformes were used for the phylogenetic analysis. The result shows that C. micropterus is closely related to Cuculus canorus bakeri. The study contributes to illuminating the taxonomic status of C. micropterus, and may facilitate further investigation of the evolution of Cuculidae.

A High-Quality Draft Genome Assembly of the Black-Necked Crane (Grus nigricollis) Based on Nanopore Sequencing.

The black-necked crane (Grus nigricollis) which inhabits high-altitude areas has the largest body size of the world's 15 crane species, and is classified as threatened by the IUCN. To support further studies on population genetics and genomics, we present a high-quality genome assembly based on both Illumina and nanopore sequencing. In total, 54.59 Gb Illumina short reads and 116.5 Gb nanopore long reads were generated. The 1.23 Gb assembled genome has a high contig N50 of 17.89 Mb, and has a longest contig of 87.83 Mb. The completeness (97.7%) of the draft genome was evaluated with single-copy orthologous genes using BUSCO. We identified 17,789 genes and found that 8.11% of the genome is composed of repetitive elements. In total, 84 of the 2,272 one-to-one orthologous genes were under positive selection in the black-necked crane lineage. SNP-based inference indicated two bottlenecks in the recent demographic trajectories of the black-necked crane. The genome information will contribute to future study of crane evolutionary history and provide new insights into the potential adaptation mechanisms of the black-necked crane to its high-altitude habitat.

The complete mitochondrial genome of Aquila nipalensis and its phylogenetic position.

Mitochondrial genome sequences are valuable resources for systematics and conservation biology studies. In this paper, we present the complete mitogenome of Aquila nipalensis which was 18,450 bp in length. The gene content and arrangement were typical for avian mtDNA. The overall A + T content of was 54.1%, and the AT skew was calculated as 0.12 for the complete mitogenome of A. nipalensis. The maximum-likelihood (ML) tree based on the concatenated 12 protein-coding genes (PCGs) revealed the basal phylogenetic position of A. nipalensis in Aquila.

Complete mitochondrial genome and the phylogenetic position of the common cuckoo, Cuculus canorus bakeri (Aves: Cuculiformes).

The complete mitochondrial genome of Common Cuckoo (Cuculus canorus bakeri) is determined in this study and was deposited in Genbank with accession number MN067867. The length of the mitogenome is 17,457 base pairs (bp) including 13 protein-coding genes (PCGs), 22 transfer (t RNA) RNA genes, two ribosomal RNA (r RNA) genes, one control region (CR) and one short pseudo-control region. The structure is similar to mitochondrial genome of other Cuculiforme species. Phylogenetic tree shows that C. canorus bakeri is closely related to C. poliocephalus. The study has provided useful information for further studies on the evolution, genetic diversity, and phylogenetic relationships in Common Cuckoo.

Application of multimodal neuroendoscopy combined with microsurgery in the surgical treatment of cystic and solid brain tumors / 中国医师进修杂志

Objective To investigate the value of multi-modal neuroendoscopy combined with microscopy in the treatment of solid cystic brain tumors. Methods Fifty patients with cystic solid tumors admitted to Wuzhou Worker′s Hospital(the Seventh Affiliated Hospital of Guangxi Medical University) from February 2016 to February 2019 were enrolled. The patients were divided into two groups by random number table method. The patients in control group (25 cases) received microsurgery, and the patients in observation group (25 cases) received microsurgery combined with neuroendoscopy. All patients underwent CT or MRI. The differences in tumor resection rate between the two groups were observed and compared. The postoperative complications and Glasgow Outcome Scale (GOS) scores were compared between the two groups. All patients were followed up for 12 months after surgery. The tumor recurrence rate and mortality rate of the two groups were compared. Results The total resection rate of the tumor in observation group was 80.00%(20/25), and in control group was 48.00%(12/25), and there was significant difference (P<0.05). The postoperative GOS score of observation group was higher than that of control group: (4.52 ± 1.73) scores vs. (3.65 ± 1.15) scores, t=2.094, P=0.041. The incidence of postoperative complications, tumor recurrence rate and the mortality rate between two groups had no significant difference (P>0.05). Conclusions Multi-modal neuroendoscopy combined with microscopy can significantly improve the total resection rate of cystic brain tumors and improve the prognosis without increasing the risk of surgery.

Effects of Supplementary Feeding on the Breeding Ecology of the Buff-Throated Partridge in a Tibetan Sacred Site, China.

Our goal was to document effects of year-round supplemental feeding on breeding ecology of the Buff-throated Partridge, Tetraophasis szechenyii, within a Tibetan sacred site. We evaluated effects of supplemental feeding used as religious/cultural practices which could potentially aid conservation of endangered phasianids. We compared fed breeding groups to neighboring nonfed groups. Fed groups initiated first clutches significantly earlier than nonfed groups. Earlier laying groups within fed and nonfed groups showed significantly lower hatching rates than later groups; however, fed groups showed significantly higher hatching rates than nonfed groups laying in the same period. Earlier laying increased opportunities to renest. All six fed groups with clutch failures renested compared to only one of five nonfed groups with clutch failures. Fed female breeders showed significantly greater investment in their young with larger clutches and larger eggs, which likely increased survivability of early hatchlings. We observed no predation on birds at feeding sites and recorded only four cases of predation on incubating females, which showed no detectable difference between fed and nonfed groups. Ground-nesting birds typically face high risks of predation. Ten of the 48 groups nested in trees, which occurs in few phasianid species. Tree nests showed significantly higher hatching rates compared to ground nests; however, we found no significant difference in tree nesting between fed and nonfed groups. This partridge is one of four gallinaceous species with cooperative breeding. Breeding groups with helpers had significantly greater reproductive success than single pairs, and fed female breeders with helpers laid bigger eggs than single pairs. Comparing annual reproductive output per group, fed groups not only produced significantly more independent young (≥ 150 days post-hatching), their young hatched significantly earlier, which likely have greater reproductive value over later hatched young of nonfed groups. Supplemental feeding year-round is likely what enabled the successes of the fed partridges.

Local villagers' perceptions of wolves in Jiuzhaigou County, western China.

While there have been increasing numbers of reports of human-wolf conflict in China during recent years, little is known about the nature of this conflict. In this study, we used questionnaires and semi-structured interviews to investigate local villagers' perceptions of wolves in Jiuzhaigou County, western China. We sampled nine villages with more frequent reports of wolf depredation to the local government, but included three villages near alpine pastures in which reports of depredation were less frequent. We sampled 100 residents, a subset of the local population who were more likely to have had experience with wolves. During the preceding three years, most families of the respondents grazed livestock on alpine pastures, and most of them reported that their livestock suffered from depredation by wolves. The mean value of the reported annual livestock loss rates was considerably higher in villages that reported depredation more frequently than in those with less frequent reports of depredation. Most respondents in the more frequently depredated villages perceived an increase in wolf populations, whereas many in the less frequently depredated villages perceived a decrease in wolf populations in their areas. People's attitudes towards wolves did not differ significantly between these two village categories. The majority of the respondents were negative in their attitude to wolves, despite a prevalent Tibetan culture that favors the protection of wildlife. People's negative attitude was directly related to the number of livestock owned by their family. Those with a larger number of livestock were more likely to have a negative attitude towards wolves. Factors such as village category, ethnicity, age and education level did not influence people's attitudes to wolves. We suggest that improved guarding of livestock and provision of monetary support on human resources and infrastructure may mitigate human-wolf conflicts in this region.

Fiber-bragg-grating-based dispersion-compensated and gain-flattened raman fiber Amplifier.

In this paper, we propose a novel signal/pump double-pass Raman fiber amplifier using fiber Brag gratings (FBGs). In order to compensate the dispersion slop mismatch among channels in lightwave system, FBGs embedded in different positions along dispersion compensated fiber are used to control the travel length of each WDM signal. Gain equalization can be achieved by optimizing the reflectivity of each FBG. Maximum output power variation among channels is less than +/-0.5 dB after appropriate optimization. Finally, a wavelength division multiplexing (WDM) system using 40-Gb/s x 8 ch non return-to-zero (NRZ) signal transmission in a 100-km transmission fiber is simulated to confirm the system performance. Using proposed dispersion compensation method, it may lead to 2 dB improvement in Q value. Such kind of RFA may find vast applications in WDM system where dispersion management is a crucial issue.