scholarly journals The Genome of Medicinal Leech (Whitmania pigra) for Exploration of Bioactive Ingredients

2020 ◽  
Author(s):  
Lei Tong ◽  
Shao-Xing Dai ◽  
De-Jun Kong ◽  
Peng-Peng Yang ◽  
Xin Tong ◽  
...  
Keyword(s):  
Gene Families ◽  
Medicinal Leech ◽  
Bioactive Molecules ◽  
Protein Coding ◽  
Helobdella Robusta ◽  
Bioactive Ingredients ◽  
Medicinal Leeches ◽  
Whitmania Pigra ◽  
Insight Into ◽  
Active Substances

Abstract BackgroundLeeches are classic annelids that have a huge diversity and closely related to people, especially medicinal leeches. Medicinal leeches have been widely utilized in medicine based on the pharmacological activities of their bioactive ingredients. The discovery of bioactive ingredients is hindered heavily due to the lack of the genome of medicinal leeches.ResultsTo facilitate this discovery and the research of medicinal leeches, we reported the first genome of the medicinal leech (Whitmania pigra). The assembled genome size of W. pigra is 177 Mbp, close to the estimated genome. Approximately about 23% of the genome was repetitive. A total of 26,743 protein-coding genes were subsequently predicted. There are only 9799 (57%) orthologous genes between W. pigra and Helobdella robusta. And only 16% genes in W. pigra showed syntenic arrangement with H. robusta revealed by gene synteny analysis. Furthermore, W. pigra and H. robusta expanded different gene families enriched in the ‘calcium ion’ and ‘sodium ion’ related functions, respectively. By inspecting genome distribution and gene structure of hirudin, we identified a new hirudin gene g17108 (hirudin_2) with different cysteine pattern. At last, we systematically explored and compared the active substances in the genomes of two leeches. The results showed that W. pigra exceeds H. robusta in both kinds and gene number of active molecules.ConclusionsThis study reported the first genome of the medicinal leech (W. pigra), which provides an important genome resource and new insight into the exploration and development of bioactive molecules of medicinal leeches.

scholarly journals The Genome of Medicinal Leech (Whitmania pigra) and comparative genomic study for Exploration of Bioactive Ingredients

2020 ◽  
Author(s):  
Lei Tong ◽  
Shao-Xing Dai ◽  
De-Jun Kong ◽  
Peng-Peng Yang ◽  
Xin Tong ◽  
...  
Keyword(s):  
Gene Families ◽  
Bioactive Molecules ◽  
Comparative Genomic ◽  
Protein Coding ◽  
Genomic Study ◽  
Comparative Genomic Study ◽  
Bioactive Ingredients ◽  
The Difference ◽  
Medicinal Leeches ◽  
Whitmania Pigra

Abstract BackgroundLeeches are classic annelids that have a huge diversity and closely related to people, especially medicinal leeches. Medicinal leeches have been widely utilized in medicine based on the pharmacological activities of their bioactive ingredients. Comparative genomic study of these leeches enables us to understand the difference among medicinal leeches and other leeches and facilitates the discovery of bioactive ingredients.ResultsIn this study, we reported the genome of Whitmania pigra and compared it with Hirudo medicinalis and Helobdella robusta. The assembled genome size of W. pigra is 177 Mbp, close to the estimated genome. Approximately about 23% of the genome was repetitive. A total of 26,743 protein-coding genes were subsequently predicted. W. pigra have 12346 (46%) and 10295 (38%) orthologous genes with H. medicinalis and H. robusta, respectively. About 20% and 24% genes in W. pigra showed syntenic arrangement with H. medicinalis and H. robusta, respectively, revealed by gene synteny analysis. Furthermore, W. pigra, H. medicinalis and H. robusta expanded different gene families enriched in different biological processes. By inspecting genome distribution and gene structure of hirudin, we identified a new hirudin gene g17108 (hirudin_2) with different cysteine pattern. Finally, we systematically explored and compared the active substances in the genomes of three leeches. The results showed that W. pigra and H. medicinalis exceed H. robusta in both kinds and gene number of active molecules.ConclusionsThis study reported the genome of W. pigra and compared it with other two leeches, which provides an important genome resource and new insight into the exploration and development of bioactive molecules of medicinal leeches.

scholarly journals High-altitude adaptation and incipient speciation in geladas

2021 ◽  
Author(s):  
Kenneth L Chiou ◽  
Mareike C Janiak ◽  
India Schneider-Crease ◽  
Sharmi Sen ◽  
Ferehiwot Ayele ◽  
...  
Keyword(s):  
High Altitude ◽  
Gene Families ◽  
Extreme Conditions ◽  
Morphometric Data ◽  
Incipient Speciation ◽  
Protein Coding ◽  
Coding Sequences ◽  
High Altitude Adaptation ◽  
Altitude Adaptation ◽  
Insight Into

Survival at high altitude requires adapting to extreme conditions such as environmental hypoxia. To understand high-altitude adaptations in a primate, we assembled the genome of the gelada (Theropithecus gelada), an endemic Ethiopian monkey, and complemented it with population resequencing, hematological, and morphometric data. Unexpectedly, we identified a novel karyotype that may contribute to reproductive isolation between gelada populations. We also identified genomic elements including protein-coding sequences and gene families that exhibit accelerated changes in geladas and may contribute to high-altitude adaptation. Our findings lend insight into mechanisms of speciation and adaptation while providing promising avenues for functional hypoxia research.

scholarly journals The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huai-Jun Xue ◽  
Yi-Wei Niu ◽  
Kari A. Segraves ◽  
Rui-E Nie ◽  
Ya-Jing Hao ◽  
...  
Keyword(s):  
Host Plant ◽  
Plant Cell Wall ◽  
Flea Beetle ◽  
Repetitive Sequences ◽  
Draft Genome ◽  
Gene Families ◽  
Ecological Speciation ◽  
Secondary Chemistry ◽  
Host Plant Specialization ◽  
Insight Into

Abstract Background Altica (Coleoptera: Chrysomelidae) is a highly diverse and taxonomically challenging flea beetle genus that has been used to address questions related to host plant specialization, reproductive isolation, and ecological speciation. To further evolutionary studies in this interesting group, here we present a draft genome of a representative specialist, Altica viridicyanea, the first Alticinae genome reported thus far. Results The genome is 864.8 Mb and consists of 4490 scaffolds with a N50 size of 557 kb, which covered 98.6% complete and 0.4% partial insect Benchmarking Universal Single-Copy Orthologs. Repetitive sequences accounted for 62.9% of the assembly, and a total of 17,730 protein-coding gene models and 2462 non-coding RNA models were predicted. To provide insight into host plant specialization of this monophagous species, we examined the key gene families involved in chemosensation, detoxification of plant secondary chemistry, and plant cell wall-degradation. Conclusions The genome assembled in this work provides an important resource for further studies on host plant adaptation and functionally affiliated genes. Moreover, this work also opens the way for comparative genomics studies among closely related Altica species, which may provide insight into the molecular evolutionary processes that occur during ecological speciation.

scholarly journals LINC01089 suppresses lung adenocarcinoma cell proliferation and migration via miR-301b-3p/STARD13 axis

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ye Qian ◽  
Yan Zhang ◽  
Haoming Ji ◽  
Yucheng Shen ◽  
Liangfeng Zheng ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Lung Adenocarcinoma ◽  
High Morbidity ◽  
Lipid Transfer ◽  
Protein Coding ◽  
Cell Proliferation And Migration ◽  
Reduce Cell Proliferation ◽  
And Migration ◽  
Insight Into ◽  
Proliferation And Migration

Abstract Background Lung adenocarcinoma (LUAD) is one of the most common cancers with high morbidity and mortality worldwide. Long non-coding RNAs (lncRNAs) serve as tumor promoters or suppressors in the development of various human malignancies, including LUAD. Although long intergenic non-protein coding RNA 1089 (LINC01089) suppresses the progression of breast cancer, its mechanism in LUAD requires further exploration. Thus, we aimed to investigate the underlying function and mechanism of LINC01089 in LUAD. Methods The expression of LINC01089 in LUAD and normal cell lines was detected. Functional assays were applied to measure cell proliferation, apoptosis and migration. Besides, mechanism experiments were employed for assessing the interplay among LINC01089, miR-301b-3p and StAR related lipid transfer domain containing 13 (STARD13). Data achieved in this study was statistically analyzed with Student’s t test or one-way analysis of variance. Results LINC01089 expression was significantly down-regulated in LUAD tissues and cells and its overexpression could reduce cell proliferation and migration. Moreover, LINC01089 could regulate STARD13 expression through competitively binding to miR-301b-3p in LUAD. Additionally, rescue assays uncovered that STARD13 depletion or miR-301b-3p overexpression could countervail the restraining effect of LINC01089 knockdown on the phenotypes of LUAD cells. Conclusion LINC01089 served as a tumor-inhibitor in LUAD by targeting miR-301b-3p/STARD13 axis, providing an innovative insight into LUAD therapies. Trial registration Not applicable.

Implementation of a Leeches + Antimicrobial Prophylaxis Order Panel to Optimize Medicinal Leech Use at a Tertiary Care Academic Medical Center

2021 ◽  
pp. 089719002199368
Author(s):  
Nicole M. Palm ◽  
Jill C. Wesolowski ◽  
Janet Y. Wu ◽  
Pavithra Srinivas
Keyword(s):  
Antimicrobial Prophylaxis ◽  
Medical Center ◽  
Academic Medical Center ◽  
Tertiary Care ◽  
Medicinal Leech ◽  
Aeromonas Species ◽  
Leech Therapy ◽  
Before And After ◽  
Timing Of Initiation ◽  
Medicinal Leeches

Medicinal leech therapy promotes vascular flow and can be used to salvage grafts. Medicinal leeches have a symbiotic relationship with Aeromonas species and can therefore present a risk of bacterial transmission to patients. Antimicrobial prophylaxis is warranted for the duration of leech therapy, however, an institutional evaluation of 40 patients receiving medicinal leech therapy demonstrated poor adherence with recommendations. An electronic medical record order panel for antimicrobial prophylaxis with medicinal leech therapy was implemented, leading to a subsequent improvement in adherence to prophylaxis use, including significant increases in the ordering of antibiotics and the appropriate timing of initiation in the subsequent 10 patients receiving medicinal leech therapy after panel implementation. Aeromonas infections were rare before and after panel implementation, and developed only in the patient subset with non-optimized prophylaxis.

scholarly journals Amynthas corticis genome reveals molecular mechanisms behind global distribution

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xing Wang ◽  
Yi Zhang ◽  
Yufeng Zhang ◽  
Mingming Kang ◽  
Yuanbo Li ◽  
...  
Keyword(s):  
Genome Assembly ◽  
Molecular Mechanisms ◽  
Gene Families ◽  
The Body ◽  
Gene Family Evolution ◽  
Complex Environments ◽  
Protein Coding ◽  
Itraq Analysis ◽  
Rdna Sequencing ◽  
Long Read

AbstractEarthworms (Annelida: Crassiclitellata) are widely distributed around the world due to their ancient origination as well as adaptation and invasion after introduction into new habitats over the past few centuries. Herein, we report a 1.2 Gb complete genome assembly of the earthworm Amynthas corticis based on a strategy combining third-generation long-read sequencing and Hi-C mapping. A total of 29,256 protein-coding genes are annotated in this genome. Analysis of resequencing data indicates that this earthworm is a triploid species. Furthermore, gene family evolution analysis shows that comprehensive expansion of gene families in the Amynthas corticis genome has produced more defensive functions compared with other species in Annelida. Quantitative proteomic iTRAQ analysis shows that expression of 147 proteins changed in the body of Amynthas corticis and 16 S rDNA sequencing shows that abundance of 28 microorganisms changed in the gut of Amynthas corticis when the earthworm was incubated with pathogenic Escherichia coli O157:H7. Our genome assembly provides abundant and valuable resources for the earthworm research community, serving as a first step toward uncovering the mysteries of this species, and may provide molecular level indicators of its powerful defensive functions, adaptation to complex environments and invasion ability.

New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update

2021 ◽  
Author(s):  
Fangfang Huang ◽  
Yingru Jiang ◽  
Tiantian Chen ◽  
Haoran Li ◽  
Mengjia Fu ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Rice Genome ◽  
Model Organism ◽  
Gene Families ◽  
Food Crop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Major Food

Abstract As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ∼2800 functionally characterized rice genes and ∼5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 49,000 users with over 490,000 page views. The funRiceGenes database has been continuously updated with newly cloned rice genes and newly published literature, based on the progress of rice functional genomics studies. Up to Nov 2021, ≥4100 functionally characterized rice genes and ∼6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new features in the last five years.

scholarly journals Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

2016 ◽  
Author(s):  
Kevin S. Bonham ◽  
Benjamin E. Wolfe ◽  
Rachel J. Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

AbstractAcquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Genome-Wide Identification of CBL-CIPK Gene Family in Honeysuckle (Lonicera japonica Thunb.) and Their Regulated Expression Under Salt Stress

2021 ◽  
Vol 12 ◽  
Author(s):  
Luyao Huang ◽  
Zhuangzhuang Li ◽  
Qingxia Fu ◽  
Conglian Liang ◽  
Zhenhua Liu ◽  
...  
Keyword(s):  
Salt Stress ◽  
Protein Kinases ◽  
Stress Responses ◽  
Structure Prediction ◽  
Functional Divergence ◽  
Gene Families ◽  
Plant Responses ◽  
Interacting Protein ◽  
Protein Motifs ◽  
Insight Into

In plants, calcineurin B-like proteins (CBLs) are a unique group of Ca2+ sensors that decode Ca2+ signals by activating a family of plant-specific protein kinases known as CBL-interacting protein kinases (CIPKs). CBL-CIPK gene families and their interacting complexes are involved in regulating plant responses to various environmental stimuli. To gain insight into the functional divergence of CBL-CIPK genes in honeysuckle, a total of six LjCBL and 17 LjCIPK genes were identified. The phylogenetic analysis along with the gene structure analysis divided both CBL and CBL-interacting protein kinase genes into four subgroups and validated by the distribution of conserved protein motifs. The 3-D structure prediction of proteins shown that most LjCBLs shared the same Protein Data Bank hit 1uhnA and most LjCIPKs shared the 6c9Da. Analysis of cis-acting elements and gene ontology implied that both LjCBL and LjCIPK genes could be involved in hormone signal responsiveness and stress adaptation. Protein-protein interaction prediction suggested that LjCBL4 is hypothesized to interact with LjCIPK7/9/15/16 and SOS1/NHX1. Gene expression analysis in response to salinity stress revealed that LjCBL2/4, LjCIPK1/15/17 under all treatments gradually increased over time until peak expression at 72 h. These results demonstrated the conservation of salt overly sensitive pathway genes in honeysuckle and a model of Ca2+-LjCBL4/LjSOS3-LjCIPK16/LjSOS2 module-mediated salt stress signaling in honeysuckle is proposed. This study provides insight into the characteristics of the CBL-CIPK gene families involved in honeysuckle salt stress responses, which could serve as a foundation for gene transformation technology, to obtain highly salt-tolerant medicinal plants in the context of the global reduction of cultivated land.

scholarly journals Effectiveness of medicinal leech therapy on infected postauricular ulcer: a case report

2020 ◽  
Vol 6 (3) ◽  
pp. 578
Author(s):  
Sinjid Ramakrishnan ◽  
Madan Bhandari ◽  
Gopikrishna B. J. ◽  
Sahanasheela K. R.
Keyword(s):  
Case Report ◽  
Medicinal Leech ◽  
High Ratio ◽  
Aesthetic Value ◽  
Leech Therapy ◽  
The Aesthetic ◽  
Medicinal Leeches

<p class="abstract">Trauma induced auricular partial defect very common. Due to the aesthetic value, proper reconstruction has to be done preserving the symmetry of bilateral auricles. The reconstruction of auricle is difficult due to the intricate anatomy of the auricle, limited and inconsistent vascularization and the high ratio of cartilage to skin. Historically, Susruta was the first author to describe about auricular repair. In Ayurveda, medicinal leech therapy is praised for it’s usefulness for the healing of ulcers. In this case report, a male of 30 years with a trauma induced postauricular infected ulcer was successfully treated with the application of medicinal leeches for multiple sittings.</p><p class="abstract"> </p>

Sign in / Sign up

Export Citation Format

Share Document