Mycolicibacterium arseniciresistens sp. nov., isolated from lead-zinc mine tailing, and reclassification of two Mycobacterium species as Mycolicibacterium palauense comb. nov. and Mycolicibacterium grossiae comb. nov.

A Gram-positive, acid-fast, aerobic, rapidly growing and non-motile strain was isolated from lead-zinc mine tailing sampled in Lanping, Yunnan province, Southwest China. 16S rRNA gene sequence analysis showed that the most closely related species of strain KC 300T was Mycolicibacterium litorale CGMCC 4.5724T (98.47 %). Additionally, phylogenomic and specific conserved signature indel analysis revealed that strain KC 300T should be a member of genus Mycolicibacterium, and Mycobacterium palauense CECT 8779T and Mycobacterium grossiae DSM 104744T should also members of genus Mycolicibacterium. The genome size of strain KC 300T was 6.2 Mb with an in silico DNA G+C content of 69.2 mol%. Chemotaxonomic characteristics of strain KC 300T were also consistent with the genus Mycolicibacterium. The average nucleotide identity, digital DNA-DNA hybridization and average amino acid identity values, as well as phenotypic, physiological and biochemical characteristics, support that strain KC 300T represents a new species within the genus Mycolicibacterium, for which the name Mycolicibacterium arseniciresistens sp. nov. is proposed, with the type strain KC 300T (=CGMCC 1.19494T=JCM 35915T). In addition, we reclassified Mycobacterium palauense and Mycobacterium grossiae as Mycolicibacterium palauense comb. nov. and Mycolicibacterium grossiae comb. nov., respectively.

The Coulomb effect in nonsequential double ionization by counter-rotating two-color elliptical polarization fields.

Using a three-dimensional classical ensemble model, nonsequential double ionization (NSDI) of Ar atoms by counter-rotating two-color elliptical polarization (TCEP) fields is investigated. The major axes of the two elliptical fields are aligned in different directions. The relative alignment of the two elliptical fields strongly affects the waveform of the combined electric field and the ultrafast dynamics of NSDI in TCEP fields. Numerical results show that the correlated electron momentum distributions in the x direction evolve from a V-shaped structure near the axis to a distribution concentrated on the diagonal with the angle between the two elliptical major axes increasing. The asymmetry of the energy sharing between the two electrons during recollision results in the V-shaped structure in the correlated momentum spectrum. Back analysis indicates that the recollision times of a part of the trajectories move from the peak to the valley of the combined electric field with the angle between the two elliptical major axes increasing. Therefore, for the case of a larger angle between the two elliptical major axes, the electrons experience a longer time to escape away from the vicinity of the parent ion and thus the stronger Coulomb effect from the parent ion makes the momentum difference between two electrons small, which results in a distribution concentrated on the diagonal. This provides an effective avenue to control the electron ultrafast dynamics in NSDI.

Chryseobacterium luquanense sp. nov., a casein-hydrolysing bacterium from the Jiaozi Mountain in Yunnan, PR China.

Strain KC 927T was isolated during an investigation of the soil bacteria diversity on Jiaozi Mountain, central Yunnan, Southwest China. The strain was Gram-stain-negative, rod-shaped, non-motile, oxidase-negative, catalase-positive and aerobic. Results of 16S rRNA gene alignment and phylogenetic analysis indicated that strain KC 927T was a member of the genus Chryseobacterium and closely related to Chryseobacterium caseinilyticum GCR10T (98.4%), Chryseobacterium piscicola DSM 21068T (98.3 %) and 'Chryseobacterium formosus' CCTCC AB 2015118T (97.9 %). With a genome size of 4 348 708 bp, strain KC 927T had 33.5 mol% DNA G+C content and contained 4012 protein-coding genes and 77 RNA genes. The average nucleotide identity and digital DNA-DNA hybridization values between strain KC 927T and C. caseinilyticum GCR10T, C. piscicola DSM 21068T and 'C. formosus' CCTCC AB 2015118T were 80.1, 79.6 and 90.7 %, and 25.5, 23.6 and 42.0 %, respectively. The main polar lipid of strain KC 927T was phosphatidylethanolamine and the respiratory quinone was MK-6. The major fatty acids (≥10 %) were iso-C15 : 0, iso-C17 : 1 ω9c and iso-C17 : 0 3-OH. Evidence from phenotypic, phylogenetic and chemotaxonomic analyses support that strain KC 927T represents a new species of the genus Chryseobacterium, for which the name Chryseobacterium luquanense sp. nov. is proposed. The type strain is KC 927T (=CGMCC 1.18760T=JCM 35707T).

The genome of medicinal leech (Whitmania pigra) and comparative genomic study for exploration of bioactive ingredients.

BACKGROUND: Leeches are classic annelids that have a huge diversity and are 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. RESULTS: In 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 size. 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 patterns. Finally, we systematically explored and compared the active substances in the genomes of three leech species. The results showed that W. pigra and H. medicinalis exceed H. robusta in both kinds and gene number of active molecules. CONCLUSIONS: This 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.

Electron correlation and recollision dynamics in nonsequential double ionization by counter-rotating two-color elliptically polarized laser fields.

Nonsequential double ionization (NSDI) of Argon atoms by counter-rotating two-color elliptically polarized (TCEP) fields is investigated with a three-dimensional classical ensemble model. Different from two-color circularly polarized fields, the combined electric field in TCEP pulses has no symmetry and the ionized electron mainly returns to the parent ion from one direction. Thus the electron momentum distributions show strong asymmetry. Numerical results show with the increase of the relative phase between the two elliptical fields, the return angle of the travelling electron, i.e., the angle between the return direction of the electron and the +x direction, gradually decreases. Moreover, the dominant behavior of electron pairs evolves from anti-correlation to correlation with the relative phase increasing. This provides an avenue to control the return angle and electron correlation behavior by the relative phase between the two elliptical fields.

Insights into gut microbiota communities of Poecilobdella manillensis, a prevalent Asian medicinal leech.

AIMS: Medicinal leeches (Annelida: Hirudinea) are fresh water ectoparasitic species which have been applied as traditional therapy. However, gut microbiota could bring high risks of opportunistic infections after leeching and arouses great interests. Here, gut bacterial and fungal communities of an Asian prevalent leech Poecilobdella manillensis were characterized and analysed through culture-independent sequencing. METHODS AND RESULTS: With high coverage in 18 samples (>0.999), a more complicated community was apparent after comparing with previous leech studies. A total of 779/939 OTUs of bacteria and fungi were detected from leech guts. The bacterial community was dominated by the phylum Bacteroidetes and Synergistetes. Genera Mucinivorans and Fretibacterium accounted mostly at the genus level, and genus Aeromonas showed an extremely low abundance (2.02%) on average. The fungal community was dominated by the phylum Ascomycota and Basidiomycota. At the genus level, the dominant OTUs included Mortierella, Geminibasidium and Fusarium. The analysis of core taxa included those above dominant genera and some low-abundance genera (>1%). The functional annotation of the bacterial community showed a close correlation with metabolism (34.8 ± 0.6%). Some fungal species were predicted as opportunistic human pathogens including Fusarium and Chaetomiaceae. CONCLUSIONS: The present study provides fundamental rationales for further studies of such issues as bacteria-fungi-host interactions, host fitness, potential pathogens, and infecting risks after leeching. It shall facilitate in-depth explorations on the safe utilization of leech therapy. SIGNIFICANCE AND IMPACT OF STUDY: Present paper is the first-ever exploration on microbiota of a prevalent Asian medicinal leech based on culture-independent technical. And it is also the first report of gut fungi community of medicinal leech. The diversity and composition of bacteria in P. manillensis was far different from that of the European leech. The main components and core OTUs indicate a particular gut environment of medicinal leech. Unknown bacterial and fungal species were also recovered from leech gut.

Siccirubricoccus soli sp. nov., a novel bacterial species isolated from Jiaozi Mountain soil.

An isolate of Gram-stain-negative and strictly aerobic bacterium, designated KC 17139T, was isolated from Jiaozi Mountain sample in Yunnan, China. Cells were non-motile cocci to oval, catalase-positive and oxidase-positive. Growth occurred at 0-7% NaCl (w/v; optimum, 0%), pH 6.0-8.0 (optimum, pH 7.0) and 15-45 °C (optimum, 28-37 °C). The polar lipids were diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC) and four unidentified aminolipids (UALs). Strain KC 17139T contained summed feature 8 (comprising C18:1 ω7c and/or C18:1 ω6c), C18:1 2OH and C16:0 as major cellular fatty acids (> 5%) and ubiquinone-10 as the sole isoprenoid quinone. The 16S rRNA gene sequence analysis indicated that strain KC 17139T shared highest similarities with Siccirubricoccus phaeus 1-3T (96.7%) and Siccirubricoccus deserti SYSU D8009T (95.0%). Strain KC 17139T clustered with the two Siccirubricoccus type strains, but formed a separate branch in both 16S rRNA gene and genome-scale phylogenetic dendrograms. The genomic DNA G + C content of strain KC 17139T was 71.2%. Genomic comparisons between strain KC 17139T and its close relatives showed the highest digital DNA-DNA hybridisation to S. phaeus (35.5%), highest average nucleotide identity to S. phaeus (88.2%), indicating that strain KC 17139T represents a novel species. On the basis of results of phenotypic, chemotaxonomic and molecular analysis, we report a new bacterium strain KC 17139T belonged to genus Siccirubricoccus, for which the name Siccirubricoccus soli sp. nov. is proposed. The type strain is KC 17139T (= CGMCC 1.18756T = JCM 35132T).

Analysis on the Vulnerability of a Tunnel Entrance under Internal Explosion.

Tunnels play an essential role in the transportation network. Tunnel entrances are usually buried at a shallow depth. In the event of an internal explosion, the blast pressure will cause severe damage or even collapse of the tunnel entrance, paralyzing the traffic system. Therefore, an accurate assessment of the damage level of tunnel entrances under internal blast loading can provide effective assistance for the anti-blast design of tunnels, post-disaster emergency response, and economic damage assessment. In this paper, four tunnel entrance specimens were designed and fabricated with a scale ratio of 1/5.5, and a series of field blast tests were carried out to examine the damage pattern of the tunnel entrances under internal explosion. Subsequently, static loading tests were conducted to obtain the maximum bearing capacity of the intact specimen and residual bearing capacities of the post-blast specimens. After that, an explicit non-linear analysis was carried out and a numerical finite element (FE) model of the tunnel entrance under internal blast loading was established by adopting the arbitrary Lagrangian-Eulerian (ALE) method and validated based on the data obtained from the field blast and static loading tests. A probabilistic vulnerability analysis of a typical tunnel entrance subjected to stochastic internal explosions (assuming various charge weights and detonation points) was then carried out with the validated FE model. For the purpose of damage assessment, the residual bearing capacity of the tunnel entrance was taken as the damage criterion. The vulnerability curves corresponding to various damage levels were further developed based on the stochastic data from the probabilistic vulnerability analysis. When the charge weight was 200 kg, the tunnel entrance exhibited slight or moderate damage, while the tunnel entrance suffered severe or even complete damage as the charge weight increased to 1000 kg. However, the tunnel entrance's probability of complete damage was less than 10% when the TNT charge weight did not exceed 1000 kg.

Infrared simulation of large-scale urban scene through LOD.

The growing use of infrared (IR) imaging systems places increasing demands for simulating infrared images of real scenes. Utilizing images captured from unmanned aerial vehicles (UAV), we propose a semi-automatic pipeline to generate large-scale IR urban scenes in the form of levels of detail (LODs). It significantly reduces the cost of labor and time while providing detailed IR structures. Starting from the surface meshes generated by multi-view stereo (MVS) systems, we produce watertight LODs via semantic segmentation and structure-aware approximation. For each LOD, we divide the surfaces into triangle facets of specific scales. For each facet, one material attribute is attached, and the heat balance equations are solved to obtain the temperature. Three strategies are proposed to accelerate the thermal distribution calculation. Finally, by synthesizing the radiance distribution, the whole IR scenes are generated and rendered. Experiments on real urban scenes show that the proposed pipeline could effectively simulate IR scenes of large-scale urban scenes.

Prohibitin is involved in the activated internalization and degradation of protease-activated receptor 1.

The protease-activated receptor 1 (PAR1) is a G-protein-coupled receptor that is irreversibly activated by either thrombin or metalloprotease 1. Due this irrevocable activation, activated internalization and degradation are critical for PAR1 signaling termination. Prohibitin (PHB) is an evolutionarily conserved, ubiquitously expressed, pleiotropic protein and belongs to the stomatin/prohibitin/flotillin/HflK/C (SPFH) domain family. In a previous study, we found that PHB localized on the platelet membrane and participated in PAR1-mediated human platelet aggregation, suggesting that PHB likely regulates the signaling of PAR1. Unfortunately, PHB's exact function in PAR1 internalization and degradation is unclear. In the current study, flow cytometry revealed that PHB expressed on the surface of endothelial cells (HUVECs) but not cancer cells (MDA-MB-231). Further confocal microscopy revealed that PHB dynamically associates with PAR1 in a time-dependent manner following induction with PAR1-activated peptide (PAR1-AP), though differently between HUVECs and MDA-MB-231 cells. Depletion of PHB by RNA interference significantly inhibited PAR1 activated internalization and led to sustained Erk1/2 phosphorylation in the HUVECs; however, a similar effect was not observed in MDA-MB-231 cells. For both the endothelial and cancel cells, PHB repressed PAR1 degradation, while knockdown of PHB led to increased PAR1 degradation, and PHB overexpression inhibited PAR1 degradation. These results suggest that persistent PAR1 signaling due to the absence of membrane PHB and decreased PAR1 degradation caused by the upregulation of intracellular PHB in cancer cells (such as MDA-MB-231 cells) may render cells highly invasive. As such, PHB may be a novel target in future anti-cancer therapeutics, or in more refined cancer malignancy diagnostics.

Progression in low-intensity ultrasound-induced tumor radiosensitization.

BACKGROUND: Radiotherapy (RT) is a widely utilized tumor treatment approach, while a significant obstacle in this treatment modality is the radioresistance exhibited by tumor cells. To enhance the effectiveness of RT, scientists have explored radiosensitization approaches, including the use of radiosensitizers and physical stimuli. Nevertheless, several approaches have exhibited disappointing results including adverse effects and limited efficacy. A safer and more effective method of radiosensitization involves low-intensity ultrasound (LIUS), which selectively targets tumor tissue and enhances the efficacy of radiation therapy. METHODS: This review summarized the tumor radioresistance reasons and explored LIUS potential radiosensitization mechanisms. Moreover, it covered diverse LIUS application strategies in radiosensitization, including the use of LIUS alone, ultrasound-targeted intravascular microbubble destruction, ultrasound-mediated targeted radiosensitizers delivery, and sonodynamic therapy. Lastly, the review presented the limitations and prospects of employing LIUS-RT combined therapy in clinical settings, emphasizing the need to connect research findings with practical applications. RESULTS AND CONCLUSION: LIUS employs cost-effective equipment to foster tumor radiosensitization, curtail radiation exposure, and elevate the quality of life for patients. This efficacy is attributed to LIUS's ability to utilize thermal, cavitation, and mechanical effects to overcome tumor cell resistance to RT. Multiple experimental analyses have underscored the effectiveness of LIUS in inducing tumor radiosensitization using diverse strategies. While initial studies have shown promising results, conducting more comprehensive clinical trials is crucial to confirm its safety and effectiveness in real-world situations.

A Chromosome-Level Genome Assembly of the Non-Hematophagous Leech Whitmania pigra (Whitman 1884): Identification and Expression Analysis of Antithrombotic Genes.

Despite being a non-hematophagous leech, Whitmania pigra is widely used in traditional Chinese medicine for the treatment of antithrombotic diseases. In this study, we provide a high quality genome of W. pigra and based on which, we performed a systematic identification of the potential antithrombotic genes and their corresponding proteins. We identified twenty antithrombotic gene families including thirteen coagulation inhibitors, three platelet aggregation inhibitors, three fibrinolysis enhancers, and one tissue penetration enhancer. Unexpectedly, a total of 79 antithrombotic genes were identified, more than a typical blood-feeding Hirudinaria manillensis, which had only 72 antithrombotic genes. In addition, combining with the RNA-seq data of W. pigra and H. manillensis, we calculated the expression levels of antithrombotic genes of the two species. Five and four gene families had significantly higher and lower expression levels in W. pigra than in H. manillensis, respectively. These results showed that the number and expression level of antithrombotic genes of a non-hematophagous leech are not always less than those of a hematophagous leech. Our study provides the most comprehensive collection of antithrombotic biomacromolecules from a non-hematophagous leech to date and will significantly enhance the investigation and utilization of leech derivatives in thrombosis therapy research and pharmaceutical applications.

The Antidiabetic Potential of Probiotics: A Review.

Diabetes has become one of the most prevalent global epidemics, significantly impacting both the economy and the health of individuals. Diabetes is associated with numerous complications, such as obesity; hyperglycemia; hypercholesterolemia; dyslipidemia; metabolic endotoxemia; intestinal barrier damage; insulin-secretion defects; increased oxidative stress; and low-grade, systemic, and chronic inflammation. Diabetes cannot be completely cured; therefore, current research has focused on developing various methods to control diabetes. A promising strategy is the use of probiotics for diabetes intervention. Probiotics are a class of live, non-toxic microorganisms that can colonize the human intestine and help improve the balance of intestinal microbiota. In this review, we summarize the current clinical studies on using probiotics to control diabetes in humans, along with mechanistic studies conducted in animal models. The primary mechanism by which probiotics regulate diabetes is improved intestinal barrier integrity, alleviated oxidative stress, enhanced immune response, increased short-chain fatty acid production, etc. Therefore, probiotic supplementation holds great potential for the prevention and management of diabetes.

Comparative genomics of two Asian medicinal leeches Hirudo nipponia and Hirudo tianjinensis: With emphasis on antithrombotic genes and their corresponding proteins.

Leeches secrete various biologically active substances which have important medical and pharmaceutical values in antithrombotic treatments. Here, we provide a high quality genome of two Asian medicinal leeches Hirudo nipponia and Hirudo tianjinensis, based on which, we identified 22 antithrombotic gene families, including fourteen coagulation inhibitors, four platelet aggregation inhibitors, three fibrinolysis enhancers, and one tissue penetration enhancer. The total numbers of antithrombotic genes were similar between H. nipponia (N = 86) and H. tianjinensis (N = 83). Molecular evolution analysis showed that no significant differences were detected between the two species in any of the three selection indices (dN, dS, and dN/dS), nor in the number of sites under positive/purifying selection. RNA-Seq based gene expression analysis showed that the overall expression patterns of the antithrombotic gene families were not significantly deviated between the two species. Our results indicated that there were rather close similarities between the two leeches on genomic characteristics, especially for the molecular evolution and expression of antithrombotic genes. Our study provides the most comprehensive collection of antithrombotic biomacromolecules from the two Asian medicinal leeches to date. These results will greatly facilitate the research and application of leech derivatives for medical and pharmaceutical purposes of thrombosis.

Observation of High-Capacity Monoclinic B-Nb2O5 with Ultrafast Lithium Storage.

Apart from Li4Ti5O12, there are few anode substitutes that can be used in commercial high-power lithium-ion batteries. Orthorhombic T-Nb2O5 has recently been proven to be another substitute anode. However, monoclinic B-Nb2O5 of same chemistry is essentially inert for lithium storage, but the underlying reasons are unclear. In order to activate the "inert" B-Nb2O5, herein, nanoporous pseudocrystals to achieve a larger specific capacity of 243 mAh g-1 than Li4Ti5O12 (theoretical capacity: 175 mAh g-1) are proposed. These pseudocrystals are rationally synthesized via a "shape-keep" topological microcorrosion process from LiNbO3 precursor. Compared to pristine B-Nb2O5, experimental investigations reveal that B-Nb2O5- x delivers ≈3000 times higher electronic conductivity and tenfold enhanced Li+ diffusion coefficient. An ≈30% reduction of energy barrier for Li-ion migration is also confirmed by the theoretical calculations. The nanoporous B-Nb2O5- x delivers unique ion/electron transport channels to proliferate the reversible and deeper lithiation, which activate the "inert" B-Nb2O5. The capacitive-like behavior is observed to endow B-Nb2O5- x ultrafast lithium storage ability, harvesting 136 mAh g-1 at 100 C and 72 mAh g-1 even at 250 C, superior to Li4Ti5O12. Pouch-type full cells exhibit the energy density of ≈251 Wh kg-1 and ultrahigh power density up to ≈35 kW kg-1.

Norisoboldine, a Natural Alkaloid from Lindera aggregata (Sims) Kosterm, Promotes Osteogenic Differentiation via S6K1 Signaling Pathway and Prevents Bone Loss in OVX Mice.

SCOPE: Norisoboldine (NOR) is a major isoquinoline alkaloid component in the traditional Chinese herbal plant Lindera aggregata (Sims) Kosterm, with previously reported anti-osteoclast differentiation and antiarthritis properties. However, the roles of NOR on osteoblasts, bone marrow mesenchymal stem cells (BMSCs), and osteoporosis in vivo have never been well established. METHODS AND RESULTS: This study investigates the ability of NOR to improve bone formation in vitro and in vivo. Osteoblasts and BMSCs are used to study the effect of NOR on osteogenic and adipogenic differentiation. It finds that NOR promotes osteogenic differentiation of osteoblasts and BMSCs, while inhibiting adipogenic differentiation of BMSCs by reducing the relative expression of peroxisome proliferator-activated receptor Î³ (Ppar-γ) and adiponectin, C1Q and collagen domain containing (Adipoq). Mechanistic studies show that NOR increases osteoblast differentiation through the mechanistic target of rapamycin kinase (mTOR)/ribosomal protein S6 kinase; polypeptide 1 (S6K1) pathway, and treatment with an mTOR inhibitor rapamycin blocked the NOR-induced increase in mineral accumulation. Finally, the study evaluates the therapeutic potential of NOR in a mouse model of ovariectomy (OVX)-induced bone loss. NOR prevents bone loss in both trabecular and cortical bone by increasing osteoblast number and phospho-S6K1 (p-S6K1) expression in osteoblasts. CONCLUSION: NOR effects in enhancing osteoblast-induced bone formation via S6K1 pathway, suggesting the potential of NOR in osteoporosis treatment by increasing bone formation.

Preparation of fish decalcified bone matrix and its bone repair effect in rats.

Decalcified bone matrix has great potential and application prospects in the repair of bone defects due to its good biocompatibility and osteogenic activity. In order to verify whether fish decalcified bone matrix (FDBM) has similar structure and efficacy, this study used the principle of HCl decalcification to prepare the FDBM by using fresh halibut bone as the raw material, and then degreasing, decalcifying, dehydrating and freeze-drying it. Its physicochemical properties were analyzed by scanning electron microscopy and other methods, and then its biocompatibility was tested by in vitro and in vivo experiments. At the same time, an animal model of femoral defect in rats was established, and commercially available bovine decalcified bone matrix (BDBM) was used as the control group, and the area of femoral defect in rats was filled with the two materials respectively. The changes in the implant material and the repair of the defect area were observed by various aspects such as imaging and histology, and its osteoinductive repair capacity and degradation properties were studied. The experiments showed that the FDBM is a form of biomaterial with high bone repair capacity and lower economic cost than other related materials such as bovine decalcified bone matrix. FDBM is simpler to extract and the raw materials are more abundant, which can greatly improve the utilization of marine resources. Our results show that FDBM not only has a good repair effect on bone defects, but also has good physicochemical properties, biosafety and cell adhesion, and is a promising medical biomaterial for the treatment of bone defects, which can basically meet the clinical requirements for bone tissue repair engineering materials.

Computational immune synapse analysis reveals T-cell interactions in distinct tumor microenvironments.

The tumor microenvironment (TME) and the cellular interactions within it can be critical to tumor progression and treatment response. Although technologies to generate multiplex images of the TME are advancing, the many ways in which TME imaging data can be mined to elucidate cellular interactions are only beginning to be realized. Here, we present a novel approach for multipronged computational immune synapse analysis (CISA) that reveals T-cell synaptic interactions from multiplex images. CISA enables automated discovery and quantification of immune synapse interactions based on the localization of proteins on cell membranes. We first demonstrate the ability of CISA to detect T-cell:APC (antigen presenting cell) synaptic interactions in two independent human melanoma imaging mass cytometry (IMC) tissue microarray datasets. We then generate melanoma histocytometry whole slide images and verify that CISA can detect similar interactions across data modalities. Interestingly, CISA histoctyometry analysis also reveals that T-cell:macrophage synapse formation is associated with T-cell proliferation. We next show the generality of CISA by extending it to breast cancer IMC images, finding that CISA quantifications of T-cell:B-cell synapses are predictive of improved patient survival. Our work demonstrates the biological and clinical significance of spatially resolving cell-cell synaptic interactions in the TME and provides a robust method to do so across imaging modalities and cancer types.

Revisiting the Asian Buffalo Leech (Hirudinaria manillensis) Genome: Focus on Antithrombotic Genes and Their Corresponding Proteins.

Leeches are well-known annelids due to their obligate blood-feeding habits. Some leech species secrete various biologically active substances which have important medical and pharmaceutical value in antithrombotic treatments. In this study, we provided a high-quality genome of the Asian buffalo leech (Hirudinaria manillensis), based on which we performed a systematic identification of potential antithrombotic genes and their corresponding proteins. Combining automatic and manual prediction, we identified 21 antithrombotic gene families including fourteen coagulation inhibitors, three platelet aggregation inhibitors, three fibrinolysis enhancers, and one tissue penetration enhancer. A total of 72 antithrombotic genes, including two pseudogenes, were identified, including most of their corresponding proteins forming three or more disulfide bonds. Three protein families (LDTI, antistasin, and granulin) had internal tandem repeats containing 6, 10, and 12 conserved cysteines, respectively. We also measured the anticoagulant activities of the five identified hirudins (hirudin_Hman1 ~ hirudin_Hman5). The results showed that three (hirudin_Hman1, hirudin_Hman2, and hirudin_Hman5), but not the remaining two, exhibited anticoagulant activities. Our study provides the most comprehensive collection of antithrombotic biomacromolecules from a leech to date. These results will greatly facilitate the research and application of leech derivatives for medical and pharmaceutical purposes in the treatment of thrombotic diseases.

Chromosome-level Dinobdella ferox genome provided a molecular model for its specific parasitism.

BACKGROUND: Dinobdella ferox is the most frequently reported leech species parasitizing the mammalian nasal cavity. However, the molecular mechanism of this special parasitic behavior has remained largely unknown. METHODS: PacBio long-read sequencing, next-generation sequencing (NGS), and Hi-C sequencing were employed in this study to generate a novel genome of D. ferox, which was annotated with strong certainty using bioinformatics methods. The phylogenetic and genomic alterations of D. ferox were then studied extensively alongside the genomes of other closely related species. The obligatory parasitism mechanism of D. ferox was investigated using RNA-seq and proteomics data. RESULTS: PacBio long-read sequencing and NGS yielded an assembly of 228 Mb and contig N50 of 2.16 Mb. Along Hi-C sequencing, 96% of the sequences were anchored to nine linkage groups and a high-quality chromosome-level genome was generated. The completed genome included 19,242 protein-coding genes. For elucidating the molecular mechanism of nasal parasitism, transcriptome data were acquired from the digestive tract and front/rear ends of D. ferox. Examining secretory proteins in D. ferox saliva helped to identify intimate connections between these proteins and membrane proteins in nasal epithelial cells. These interacting proteins played important roles in extracellular matrix (ECM)-receptor interaction, tight junction, focal adhesion, and adherens junction. The interaction between D. ferox and mammalian nasal epithelial cells included three major steps of pattern recognition, mucin connection and breakdown, and repair of ECM. The remodeling of ECM between epithelial cells of the nasal mucosa and epithelial cells of D. ferox may produce a stable adhesion environment for parasitism. CONCLUSIONS: Our study represents the first-ever attempt to propose a molecular model for specific parasitism. This molecular model may serve as a practical reference for parasitism models of other species and a theoretical foundation for a molecular process of parasitism.