Computational modeling guides tissue-engineered heart valve design for long-term in vivo performance in a translational sheep model

Content introduction:

• Computational modeling guides tissue-engineered heart valve design for long-term in vivo performance in a translational sheep model


• Survival of syngeneic and allogeneic iPSC–derived neural precursors after spinal grafting in minipigs


• High-throughput sequencing of the T cell receptor β gene identifies aggressive early-stage mycosis fungoides


• PGD2/DP2 receptor activation promotes severe viral bronchiolitis by suppressing IFN-λ production


• Global assessment of its network dynamics reveals that the kinase Plk1 inhibits the phosphatase PP6 to promote Aurora A activity

1. Computational modeling guides tissue-engineered heart valve design for long-term in vivo performance in a translational sheep model

Valvular heart disease is a major cause of morbidity and mortality worldwide. Current heart valve prostheses have considerable clinical limitations due to their artificial, nonliving nature without regenerative capacity. To overcome these limitations, heart valve tissue engineering (TE) aiming to develop living, native-like heart valves with self-repair, remodeling, and regeneration capacity has been suggested as next-generation technology. A major roadblock to clinically relevant, safe, and robust TE solutions has been the high complexity and variability inherent to bioengineering approaches that rely on cell-driven tissue remodeling. For heart valve TE, this has limited long-term performance in vivo because of uncontrolled tissue remodeling phenomena, such as valve leaflet shortening, which often translates into valve failure regardless of the bioengineering methodology used to develop the implant. Maximilian Y. Emmert at University of Zurich in Zurich, Switzerland and his colleagues tested the hypothesis that integration of a computationally inspired heart valve design into their TE methodologies could guide tissue remodeling toward long-term functionality in tissue-engineered heart valves (TEHVs). In a clinically and regulatory relevant sheep model, TEHVs implanted as pulmonary valve replacements using minimally invasive techniques were monitored for 1 year via multimodal in vivo imaging and comprehensive tissue remodeling assessments. TEHVs exhibited good preserved long-term in vivo performance and remodeling comparable to native heart valves, as predicted by and consistent with computational modeling. TEHV failure could be predicted for nonphysiological pressure loading. Beyond previous studies, this work suggests the relevance of an integrated in silico, in vitro, and in vivo bioengineering approach as a basis for the safe and efficient clinical translation of TEHVs.


Read more, please click http://stm.sciencemag.org/content/10/440/eaan4587

2. Survival of syngeneic and allogeneic iPSC–derived neural precursors after spinal grafting in minipigs

The use of autologous (or syngeneic) cells derived from induced pluripotent stem cells (iPSCs) holds great promise for future clinical use in a wide range of diseases and injuries. It is expected that cell replacement therapies using autologous cells would forego the need for immunosuppression, otherwise required in allogeneic transplantations. However, recent studies have shown the unexpected immune rejection of undifferentiated autologous mouse iPSCs after transplantation. Whether similar immunogenic properties are maintained in iPSC-derived lineage-committed cells (such as neural precursors) is relatively unknown. Jan Strnadel at University of California in San Diego, USA and his colleagues demonstrate that syngeneic porcine iPSC-derived neural precursor cell (NPC) transplantation to the spinal cord in the absence of immunosuppression is associated with long-term survival and neuronal and glial differentiation. No tumor formation was noted. Similar cell engraftment and differentiation were shown in spinally injured transiently immunosuppressed swine leukocyte antigen (SLA)–mismatched allogeneic pigs. These data demonstrate that iPSC-NPCs can be grafted into syngeneic recipients in the absence of immunosuppression and that temporary immunosuppression is sufficient to induce long-term immune tolerance after NPC engraftment into spinally injured allogeneic recipients. Collectively, their results show that iPSC-NPCs represent an alternative source of transplantable NPCs for the treatment of a variety of disorders affecting the spinal cord, including trauma, ischemia, or amyotrophic lateral sclerosis.

Read more, please click http://stm.sciencemag.org/content/10/440/eaam6651

3. High-throughput sequencing of the T cell receptor β gene identifies aggressive early-stage mycosis fungoides

Mycosis fungoides (MF), the most common cutaneous T cell lymphoma (CTCL) is a malignancy of skin-tropic memory T cells. Most MF cases present as early stage (stage I A/B, limited to the skin), and these patients typically have a chronic, indolent clinical course. However, a small subset of early-stage cases develop progressive and fatal disease. Because outcomes can be so different, early identification of this high-risk population is an urgent unmet clinical need. Adele de Masson at Harvard Medical School in Boston, USA and his colleagues evaluated the use of next-generation high-throughput DNA sequencing of the T cell receptor β gene (TCRB) in lesional skin biopsies to predict progression and survival in a discovery cohort of 208 patients with CTCL (177 with MF) from a 15-year longitudinal observational clinical study. They compared these data to the results in an independent validation cohort of 101 CTCL patients (87 with MF). The tumor clone frequency (TCF) in lesional skin, measured by high-throughput sequencing of the TCRB gene, was an independent prognostic factor of both progression-free and overall survival in patients with CTCL and MF in particular. In early-stage patients, a TCF of >25% in the skin was a stronger predictor of progression than any other established prognostic factor (stage IB versus IA, presence of plaques, high blood lactate dehydrogenase concentration, large-cell transformation, or age). The TCF therefore may accurately predict disease progression in early-stage MF. Early identification of patients at high risk for progression could help identify candidates who may benefit from allogeneic hematopoietic stem cell transplantation before their disease becomes treatment-refractory.

Read more, please click http://stm.sciencemag.org/content/10/440/eaar5894

4. PGD2/DP2 receptor activation promotes severe viral bronchiolitis by suppressing IFN-λ production

Prostaglandin D2 (PGD2) signals through PGD2 receptor 2 (DP2, also known as CRTH2) on type 2 effector cells to promote asthma pathogenesis; however, little is known about its role during respiratory syncytial virus (RSV) bronchiolitis, a major risk factor for asthma development. Rhiannon B. Werder at University of Queensland in Queensland, Australia and his colleagues show that RSV infection up-regulated hematopoietic prostaglandin D synthase expression and increased PGD2 release by cultured human primary airway epithelial cells (AECs). Moreover, PGD2 production was elevated in nasopharyngeal samples from young infants hospitalized with RSV bronchiolitis compared to healthy controls. In a neonatal mouse model of severe viral bronchiolitis, DP2 antagonism decreased viral load, immunopathology, and morbidity and ablated the predisposition for subsequent asthma onset in later life. This protective response was abolished upon dual DP1/DP2 antagonism and replicated with a specific DP1 agonist. Rather than mediating an effect via type 2 inflammation, the beneficial effects of DP2 blockade or DP1 agonism were associated with increased interferon-λ (IFN-λ) [interleukin-28A/B (IL-28A/B)] expression and were lost upon IL-28A neutralization. In RSV-infected AEC cultures, DP1 activation up-regulated IFN-λ production, which, in turn, increased IFN-stimulated gene expression, accelerating viral clearance. Their findings suggest that DP2 antagonists or DP1 agonists may be useful antivirals for the treatment of viral bronchiolitis and possibly as primary preventatives for asthma.

Read more, please click http://stm.sciencemag.org/content/10/440/eaao0052

5. Global assessment of its network dynamics reveals that the kinase Plk1 inhibits the phosphatase PP6 to promote Aurora A activity

Polo-like kinase 1 (Plk1) is an essential protein kinase that promotes faithful mitotic progression in eukaryotes. The subcellular localization and substrate interactions of Plk1 are tightly controlled and require its binding to phosphorylated residues. To identify phosphorylation-dependent interactions within the Plk1 network in human mitotic cells, Arminja N. Kettenbach at Geisel School of Medicine at Dartmouth in Hanover, USA and his colleagues performed quantitative proteomics on HeLa cells cultured with kinase inhibitors or expressing a Plk1 mutant that was deficient in phosphorylation-dependent substrate binding. They found that many interactions were abolished upon kinase inhibition; however, a subset was protected from phosphatase opposition or was unopposed, resulting in persistent interaction of the substrate with Plk1. This subset includes phosphoprotein phosphatase 6 (PP6), whose activity toward Aurora kinase A (Aurora A) was inhibited by Plk1. Their data suggest that this Plk1-PP6 interaction generates a feedback loop that coordinates and reinforces the activities of Plk1 and Aurora A during mitotic entry and is terminated by the degradation of Plk1 during mitotic exit. Thus, they have identified a mechanism for the previously puzzling observation of the Plk1-dependent regulation of Aurora A.

Read more, please click http://stke.sciencemag.org/content/11/530/eaaq1441

Apoptosis Assays

Apoptosis is is a process of programmed cell death that biochemical events lead to characteristic cell changes, including compaction of the nuclear chromatin, shrinkage of the cytoplasm and production of membrane-bound apoptotic bodies. As with cell viability, no single parameter fully defines cell death in all systems; therefore, it is often recommended to use several different methods when studying apoptosis. There are also various biochemical techniques for analysis of cell surface markers (phosphatidylserine exposure versus cell permeability by flow cytometry), cellular markers such as DNA fragmentation, caspase activation, Bid cleavage, and cytochrome c release (Western blotting) for analysis of apoptotic cells. Anti-cancer drug candidates failing to induce apoptosis are likely to have decreased clinical efficacy, making apoptosis assays important tools for high-throughput drug screening.

Last time, we discussed using highly fluorescent annexin V conjugates to detect apoptosis based on membrane phospholipid asymmetry changes during apoptosis. Here we decribe several assays using nucleic acid stains for detecting apoptotic cells.

Part1: Comet (Single-Cell Gel Electrophoresis) Assay to Detect Damaged DNA

The comet assay (single-cell gel electrophoresis) is a useful technique for studying DNA damage and repair with manifold applications. It was first developed by Östling & Johansson in 1984 and later modified by Singh et al. in 1988. Cells are immobilized in a thin agarose matrix on slides,  and then these embedded cells are then treated with a lysis buffer and alkaline solution, which relaxes and denatures the DNA. When subjected to electrophoresis, the unwound, relaxed DNA migrates out of the cells. Following electrophoresis, the samples are dried, stained with a DNA dye, and visualized by epifluorescence microscopy (Figure 1). Comet assays have traditionally been performed using ethidium bromide to stain the DNA; however, use of the SYBR Gold and SYBR Green I stains ref improves the sensitivity of this assay.

Figure 1. Scheme for the performance of the comet assay

After staining with a nucleic acid stain, cells that have accumulated DNA damage appear as fluorescent comets, with tails of DNA fragmentation or unwinding. In contrast, cells with normal, undamaged DNA appear as round dots, because their intact DNA does not migrate out of the cell (Figure 2).

Figure 2. Typical result of Comet Assay

The comet assay is an extremely sensitive DNA damage assay. This sensitivity needs to be handled carefully as it is also vulnerable to physical changes which can affect the reproducibility of results. Essentially, anything that can cause DNA damage or denaturation except the factor(s) being researched is to be avoided. The most common form of the assay is the alkaline version, introduced by Singh and coworkers, detects a broad spectrum of DNA lesions, that is, DNA single- and double-strand breaks and alkalilabile sites. Due to its simple and inexpensive setup, it can be used in conditions where more complex assays are not available.

To be continued....

Q3

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How to distinguish apoptosis from necrosis?

Apoptosis is a form of programmed cell death that is used by the body to remove unwanted, damaged, or senescent cells from tissues. In normal cells, the negative phospholipids reside on the inner side of the cellular membrane while the outer surface of the membrane is occupied by uncharged phospholipids. After a cell has entered apoptosis, the negatively charged phospholipids (PS) are transported to the outer cell surface by a hypothetical protein known as scramblase. Phagocytic white blood cells express a receptor that can bind to and detect the negatively charged phospholipids on the apoptotic cell surfaces. After detection, the apoptotic cells are removed. Necrosis has been characterized as passive, accidental cell death resulting from environmental perturbations with uncontrolled release of inflammatory cellular contents.

Annexin Ⅴ is a Ca²⁺ dependent phospholipid binding protein with a molecular weight of 35-36 KD, which can specifically bind to PS on the outer cell suiface with high affinity during apoptosis. Labeling of Annexin Ⅴ with fluorescent or radioactive molecules makes it possible to detect binding of labeled Annexin Ⅴ to the cell surface of apoptotic cells. After binding to the phospholipid surface, Annexin Ⅴ assembles into a trimeric cluster. This trimer consists of three Annexin Ⅴ molecules that are bound to each other via non-covalent protein-protein interactions. The formation of Annexin Ⅴ trimers results in the formation of a two-dimensional crystal lattice on the phospholipid membrane. This clustering of Annexin Ⅴ on the membrane greatly increases the intensity of Annexin Ⅴ when labeled with a fluorescent or radioactive probe. Propidium iodide (or PI) is a fluorescent nucleus dye, impermeant to live cells and apoptotic cells, but stains dead cells with red fluorescence, binding tightly to the nucleic acids in the cell. In molecular biology,  is a test to quantify the number of cells undergoing apoptosis. The assay uses the protein Annexin Ⅴ to tag apoptotic and dead cells, and the numbers are then counted using either flow cytometry or a fluorescence microscope.

Figure 1. Annexin V-FITC and pyridine iodide staining of L-929 Cells

In molecular biology, combining AnnexinⅤlabeling with fluorescent with PI can distinguish apoptosis from necrosis: Live cells (AnnexinⅤand PI both negative); Apoptonic cells (AnnexinⅤpositive, PI negative); Necrotic cells (AnnexinⅤand PI both positive). The one-step staining procedure takes only 10--15 minutes. Detection can be analyzed by flow cytometry or by fluorescence microscopy (Figure 1).

How does salinomycin act on cancer stem cells- a fluorescent variant shows the mechanism

Salinomycin is a molecule produced by terrestrial bacteria of the species Streptomyces albus. It was previously known that this molecule acts selectively against cancer stem cells. Salinomycin has been shown to kill breast cancer stem cells in mice at least 100 times more effectively than the anti-cancer drug paclitaxel. The mechanism of action by which salinomycin kills cancer stem cells remains unknown, but is thought to be due to its action as a potassium ionophore due to the detection of nigericin in the same compound screen.

Now, researchers from Lund University have created a fluorescent variant of salinomycin to understand how it works. Capturing images of when the molecule enters a cell has enabled the researchers, using cell-biological methods, to successfully describe how and where the molecule counteracts the cancer stem cells. An active fluorescent salinomycin conjugate reveals rapid cellular uptake and strong localization to the endoplasmic reticulum. Ionophore activity in this organelle is connected to phenotype effects.

Synthesis and Cellular Uptake of Fluorescent Salinomycin Conjugates

To visualize cellular uptake and subcellular localization of salinomycin, a fluorescent conjugate that was functionally equivalent to the native structure is needed to design. Selective ligation of fluorophores to complex natural products like salinomycin without impairing their properties is nontrivial.

Experiments demonstrated that ligation of a nitrobenzoxadiazole(NBD) reporter to the C20 hydroxyl of salinomycin gives a fluorescent conjugate that is functionally equivalent to salinomycin and hence suitable for mechanistic investigations. The real-time uptake experiments moreover revealed salinomycin derivatives entering cells on a time scale that supports using such structures for acute cell experiments.

Salinomycin Accumulates in the Endoplasmic Reticulum and in Lipid Droplets

The subcellular localization of salinomycin conjugates in breast cancer cells was investigated using confocal microscopy.

LDs are lipophilic structures that originate from lipid deposits in the ER phospholipid bilayer and thus share many of its characteristics. They interpret the preferential accumulation of the conjugates in the ER and LDs as a reflection of their lipophilic nature. Combined with the observation that only salinomycin derivatives capable of electroneutral alkali metal ion transport induces phenotype effects, the localization data indicate that the principal function of salinomycin is ionophore activity in the ER membrane.

Salinomycin Induces ER Ca2+ Release, ER Stress, and PKC Activation

Accumulation of salinomycin in the ER suggests that its ion transport properties may underlie its effect on the cytosolic Ca2+ concentration. The Ca2+ source contributing to the increase in cytosolic Ca2+ caused by salinomycin was thus investigated.

Combined, the data show that salinomycin causes an increase in the release of Ca2+ from the ER. This release ultimately results in an increase in CHOP expression and activation of calcium-dependent PKC, both known factors contributing to inhibition of Wnt signaling.

Conclusion

Scientists developed a fluorescent NBD conjugate of salinomycin that retains the activity profile of the native structure. This conjugate was used to guide a mechanistic investigation of the molecular basis for the activity of salinomycin against stemlike cancer cells. The conjugate was shown to rapidly enter breast cancer cells and localize in the ER and LDs. Uptake of salinomycin into the ER was then shown to result in an enhanced Ca2+ release from this organelle, presumably a result of a counter transport of K+ by salinomycin. Depletion of Ca2+ from the ER led to ER stress and activation of the UPR, which induced up-regulation of CHOP. The concomitant increase in cytosolic Ca2+ caused activation of conventional PKCs. Since both up-regulation of CHOP and activation of PKC inhibit the Wnt signaling pathway, they connects the mechanism of salinomycin at the molecular level to previously described phenotype effects.

The research results may contribute new approaches to the development of cancer drugs both for treatment of cancer and for reducing the risk of relapse.

More information, please click https://www.lunduniversity.lu.se/article/fluorescent-molecules-reveal-how-cancer-stem-cells-are-selectively-inhibited

The Nobel Prize in Physiology or Medicine 2016

Yoshinori Ohsumi

Born: 9 February 1945, Fukuoka, Japan

Affiliation at the time of the award: Tokyo Institute of Technology, Tokyo, Japan

Prize motivation: "for his discoveries of mechanisms for autophagy"

Life

Yoshinori Ohsumi was born in Fukuoka, Japan. He studied at the University of Tokyo where he received his doctoral degree in 1974. After a few years at Rockefeller University, New York, he returned to the University of Tokyo. In 1996 he moved to the National Institute for Basic Biology in Okazaki. He has also been affiliated to the Graduate University for Advanced Studies (Sokendai) in Hayama and to the Tokyo Institute of Technology, where he is now working. Yoshinori Ohsumi is married to Mariko Ohsumi who is also one of his scientific collaborators.

Work

In the lysosomes of our cells its components are processed for reuse. The mechanisms of this process were mostly unknown until the early 1990s, when Yoshinori Ohsumi conducted a series of groundbreaking experiments with yeast, where he detected autophagy and identified genes important for the process. Yoshinori Ohsumi's discoveries laid the foundation for a better understanding of the ability of cells to manage malnutrition and infections, the causes of certain hereditary and neurological diseases, and cancer.



More details, please click The Nobel Prize in Physiology or Medicine 2016.

How does salinomycin act on cancer stem cells- a fluorescent variant shows the mechanism

Salinomycin is a molecule produced by terrestrial bacteria of the species Streptomyces albus. It was previously known that this molecule acts selectively against cancer stem cells. Salinomycin has been shown to kill breast cancer stem cells in mice at least 100 times more effectively than the anti-cancer drug paclitaxel. The mechanism of action by which salinomycin kills cancer stem cells remains unknown, but is thought to be due to its action as a potassium ionophore due to the detection of nigericin in the same compound screen.

Now, researchers from Lund University have created a fluorescent variant of salinomycin to understand how it works. Capturing images of when the molecule enters a cell has enabled the researchers, using cell-biological methods, to successfully describe how and where the molecule counteracts the cancer stem cells. An active fluorescent salinomycin conjugate reveals rapid cellular uptake and strong localization to the endoplasmic reticulum. Ionophore activity in this organelle is connected to phenotype effects.

Synthesis and Cellular Uptake of Fluorescent Salinomycin Conjugates

To visualize cellular uptake and subcellular localization of salinomycin, a fluorescent conjugate that was functionally equivalent to the native structure is needed to design. Selective ligation of fluorophores to complex natural products like salinomycin without impairing their properties is nontrivial.

Experiments demonstrated that ligation of a nitrobenzoxadiazole(NBD) reporter to the C20 hydroxyl of salinomycin gives a fluorescent conjugate that is functionally equivalent to salinomycin and hence suitable for mechanistic investigations. The real-time uptake experiments moreover revealed salinomycin derivatives entering cells on a time scale that supports using such structures for acute cell experiments.

Salinomycin Accumulates in the Endoplasmic Reticulum and in Lipid Droplets

The subcellular localization of salinomycin conjugates in breast cancer cells was investigated using confocal microscopy.

LDs are lipophilic structures that originate from lipid deposits in the ER phospholipid bilayer and thus share many of its characteristics. They interpret the preferential accumulation of the conjugates in the ER and LDs as a reflection of their lipophilic nature. Combined with the observation that only salinomycin derivatives capable of electroneutral alkali metal ion transport induces phenotype effects, the localization data indicate that the principal function of salinomycin is ionophore activity in the ER membrane.

Salinomycin Induces ER Ca2+ Release, ER Stress, and PKC Activation

Accumulation of salinomycin in the ER suggests that its ion transport properties may underlie its effect on the cytosolic Ca2+ concentration. The Ca2+ source contributing to the increase in cytosolic Ca2+ caused by salinomycin was thus investigated.

Combined, the data show that salinomycin causes an increase in the release of Ca2+ from the ER. This release ultimately results in an increase in CHOP expression and activation of calcium-dependent PKC, both known factors contributing to inhibition of Wnt signaling.

Conclusion

Scientists developed a fluorescent NBD conjugate of salinomycin that retains the activity profile of the native structure. This conjugate was used to guide a mechanistic investigation of the molecular basis for the activity of salinomycin against stemlike cancer cells. The conjugate was shown to rapidly enter breast cancer cells and localize in the ER and LDs. Uptake of salinomycin into the ER was then shown to result in an enhanced Ca2+ release from this organelle, presumably a result of a counter transport of K+ by salinomycin. Depletion of Ca2+ from the ER led to ER stress and activation of the UPR, which induced up-regulation of CHOP. The concomitant increase in cytosolic Ca2+ caused activation of conventional PKCs. Since both up-regulation of CHOP and activation of PKC inhibit the Wnt signaling pathway, they connects the mechanism of salinomycin at the molecular level to previously described phenotype effects.

The research results may contribute new approaches to the development of cancer drugs both for treatment of cancer and for reducing the risk of relapse.

More information, please click https://www.lunduniversity.lu.se/article/fluorescent-molecules-reveal-how-cancer-stem-cells-are-selectively-inhibited

How does salinomycin act on cancer stem cells- a fluorescent variant shows the mechanism

Salinomycin is a molecule produced by terrestrial bacteria of the species Streptomyces albus. It was previously known that this molecule acts selectively against cancer stem cells. Salinomycin has been shown to kill breast cancer stem cells in mice at least 100 times more effectively than the anti-cancer drug paclitaxel. The mechanism of action by which salinomycin kills cancer stem cells remains unknown, but is thought to be due to its action as a potassium ionophore due to the detection of nigericin in the same compound screen.

Now, researchers from Lund University have created a fluorescent variant of salinomycin to understand how it works. Capturing images of when the molecule enters a cell has enabled the researchers, using cell-biological methods, to successfully describe how and where the molecule counteracts the cancer stem cells. An active fluorescent salinomycin conjugate reveals rapid cellular uptake and strong localization to the endoplasmic reticulum. Ionophore activity in this organelle is connected to phenotype effects.

Synthesis and Cellular Uptake of Fluorescent Salinomycin Conjugates

To visualize cellular uptake and subcellular localization of salinomycin, a fluorescent conjugate that was functionally equivalent to the native structure is needed to design. Selective ligation of fluorophores to complex natural products like salinomycin without impairing their properties is nontrivial.

Experiments demonstrated that ligation of a nitrobenzoxadiazole(NBD) reporter to the C20 hydroxyl of salinomycin gives a fluorescent conjugate that is functionally equivalent to salinomycin and hence suitable for mechanistic investigations. The real-time uptake experiments moreover revealed salinomycin derivatives entering cells on a time scale that supports using such structures for acute cell experiments.

Salinomycin Accumulates in the Endoplasmic Reticulum and in Lipid Droplets

The subcellular localization of salinomycin conjugates in breast cancer cells was investigated using confocal microscopy.

LDs are lipophilic structures that originate from lipid deposits in the ER phospholipid bilayer and thus share many of its characteristics. They interpret the preferential accumulation of the conjugates in the ER and LDs as a reflection of their lipophilic nature. Combined with the observation that only salinomycin derivatives capable of electroneutral alkali metal ion transport induces phenotype effects, the localization data indicate that the principal function of salinomycin is ionophore activity in the ER membrane.

Salinomycin Induces ER Ca2+ Release, ER Stress, and PKC Activation

Accumulation of salinomycin in the ER suggests that its ion transport properties may underlie its effect on the cytosolic Ca2+ concentration. The Ca2+ source contributing to the increase in cytosolic Ca2+ caused by salinomycin was thus investigated.

Combined, the data show that salinomycin causes an increase in the release of Ca2+ from the ER. This release ultimately results in an increase in CHOP expression and activation of calcium-dependent PKC, both known factors contributing to inhibition of Wnt signaling.

Conclusion

Scientists developed a fluorescent NBD conjugate of salinomycin that retains the activity profile of the native structure. This conjugate was used to guide a mechanistic investigation of the molecular basis for the activity of salinomycin against stemlike cancer cells. The conjugate was shown to rapidly enter breast cancer cells and localize in the ER and LDs. Uptake of salinomycin into the ER was then shown to result in an enhanced Ca2+ release from this organelle, presumably a result of a counter transport of K+ by salinomycin. Depletion of Ca2+ from the ER led to ER stress and activation of the UPR, which induced up-regulation of CHOP. The concomitant increase in cytosolic Ca2+ caused activation of conventional PKCs. Since both up-regulation of CHOP and activation of PKC inhibit the Wnt signaling pathway, they connects the mechanism of salinomycin at the molecular level to previously described phenotype effects.

The research results may contribute new approaches to the development of cancer drugs both for treatment of cancer and for reducing the risk of relapse.

More information, please click https://www.lunduniversity.lu.se/article/fluorescent-molecules-reveal-how-cancer-stem-cells-are-selectively-inhibited

The Nobel Prize in Physiology or Medicine 2016

Yoshinori Ohsumi

Born: 9 February 1945, Fukuoka, Japan

Affiliation at the time of the award: Tokyo Institute of Technology, Tokyo, Japan

Prize motivation: "for his discoveries of mechanisms for autophagy"

Life

Yoshinori Ohsumi was born in Fukuoka, Japan. He studied at the University of Tokyo where he received his doctoral degree in 1974. After a few years at Rockefeller University, New York, he returned to the University of Tokyo. In 1996 he moved to the National Institute for Basic Biology in Okazaki. He has also been affiliated to the Graduate University for Advanced Studies (Sokendai) in Hayama and to the Tokyo Institute of Technology, where he is now working. Yoshinori Ohsumi is married to Mariko Ohsumi who is also one of his scientific collaborators.

Work

In the lysosomes of our cells its components are processed for reuse. The mechanisms of this process were mostly unknown until the early 1990s, when Yoshinori Ohsumi conducted a series of groundbreaking experiments with yeast, where he detected autophagy and identified genes important for the process. Yoshinori Ohsumi's discoveries laid the foundation for a better understanding of the ability of cells to manage malnutrition and infections, the causes of certain hereditary and neurological diseases, and cancer.



More details, please click The Nobel Prize in Physiology or Medicine 2016.

Abbkine full portfolio of loading control and epitope tag antibodies

With full portfolio of loading control and epitope tag antibodies, Abbkine launched series of conjugated antibodies, including HRP, Biotin, FITC, Cy3 and AbFluor™ dyes to meet the diversified demands of researchers. Also, the agarose and magnetic beads conjugated tag antibodies specifically for immunoprecipitation are now available.

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Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury

Content introduction：

• A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers


• lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer


• Genomic and Functional Approaches to Understanding Cancer Aneuploidy


• Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury


• Large-Scale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment

1. A Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers

Ashton C. Berger at The Eli and Edythe L. Broad Institute of Massachusetts Institute of Technology and Harvard University in Cambridge, USA and his colleagues analyzed molecular data on 2,579 tumors from The Cancer Genome Atlas (TCGA) of four gynecological types plus breast. Their aims were to identify shared and unique molecular features, clinically significant subtypes, and potential therapeutic targets. They found 61 somatic copy-number alterations (SCNAs) and 46 significantly mutated genes (SMGs). Eleven SCNAs and 11 SMGs had not been identified in previous TCGA studies of the individual tumor types. They found functionally significant estrogen receptor-regulated long non-coding RNAs (lncRNAs) and gene/lncRNA interaction networks. Pathway analysis identified subtypes with high leukocyte infiltration, raising potential implications for immunotherapy. Using 16 key molecular features, they identified five prognostic subtypes and developed a decision tree that classified patients into the subtypes based on just six features that are assessable in clinical laboratories.

Read more, please click https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30119-3

2. lncRNA Epigenetic Landscape Analysis Identifies EPIC1 as an Oncogenic lncRNA that Interacts with MYC and Promotes Cell-Cycle Progression in Cancer

Zehua Wang at Department of Pharmaceutical Sciences, University of Pittsburgh in Pittsburgh, USA and his colleagues characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to the CpG island hypermethylation phenotype in cancer, they observed a recurrent hypomethylation of 1,006 lncRNA genes in cancer, including EPIC1 (epigenetically-induced lncRNA1). Overexpression of EPIC1 is associated with poor prognosis in luminal B breast cancer patients and enhances tumor growth in vitro and in vivo. Mechanistically, EPIC1 promotes cell-cycle progression by interacting with MYC through EPIC1's 129–283 nt region. EPIC1 knockdown reduces the occupancy of MYC to its target genes (e.g., CDKN1A, CCNA2, CDC20, and CDC45). MYC depletion abolishes EPIC1's regulation of MYC target and luminal breast cancer tumorigenesis in vitro and in vivo.

Read more, please click https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30110-7

3. Genomic and Functional Approaches to Understanding Cancer Aneuploidy

Aneuploidy, whole chromosome or chromosome arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression of proliferation genes. Aneuploidy was anti-correlated with expression of immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss of chromosome arm 3p in squamous cancers. Alison M. Taylor at Department of Medical Oncology, Dana-Farber Cancer Institute in Boston, USA and his colleagues applied genome engineering to delete 3p in lung cells, causing decreased proliferation rescued in part by chromosome 3 duplication. This study defines genomic and phenotypic correlates of cancer aneuploidy and provides an experimental approach to study chromosome arm aneuploidy.

Read more, please click https://www.cell.com/cancer-cell/fulltext/S1535-6108(18)30111-9

4. Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury

Cells demonstrate plasticity following injury, but the extent of this phenomenon and the cellular mechanisms involved remain underexplored. Using single-cell RNA sequencing (scRNA-seq) and lineage tracing, Aleksandra Tata at Duke University School of Medicine in Durham, USA and his colleagues uncover that myoepithelial cells (MECs) of the submucosal glands (SMGs) proliferate and migrate to repopulate the airway surface epithelium (SE) in multiple injury models. Specifically, SMG-derived cells display multipotency and contribute to basal and luminal cell types of the SMGs and SE. Ex vivo expanded MECs have the potential to repopulate and differentiate into SE cells when grafted onto denuded airway scaffolds. Significantly, they find that SMG-like cells appear on the SE of both extra- and intra-lobular airways of large animal lungs following severe injury. They find that the transcription factor SOX9 is necessary for MEC plasticity in airway regeneration. Because SMGs are abundant and present deep within airways, they may serve as a reserve cell source for enhancing human airway regeneration.



Read more, please click https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30124-3

5. Large-Scale Clonal Analysis Resolves Aging of the Mouse Hematopoietic Stem Cell Compartment

Aging is linked to functional deterioration and hematological diseases. The hematopoietic system is maintained by hematopoietic stem cells (HSCs), and dysfunction within the HSC compartment is thought to be a key mechanism underlying age-related hematopoietic perturbations. Using single-cell transplantation assays with five blood-lineage analysis, Ryo Yamamoto at Stanford University School of Medicine in Stanford, USA and his colleagues previously identified myeloid-restricted repopulating progenitors (MyRPs) within the phenotypic HSC compartment in young mice. Here, they determined the age-related functional changes to the HSC compartment using over 400 single-cell transplantation assays. Notably, MyRP frequency increased dramatically with age, while multipotent HSCs expanded modestly within the bone marrow. They also identified a subset of functional cells that were myeloid restricted in primary recipients but displayed multipotent (five blood-lineage) output in secondary recipients. They have termed this cell type latent-HSCs, which appear exclusive to the aged HSC compartment. These results question the traditional dogma of HSC aging and our current approaches to assay and define HSCs.

Read more, please click https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(18)30119-X

Abbkine new arrival-Annexin V Apoptosis Detection kit

Apoptosis is a form of programmed cell death to remove unwanted, damaged, or senescent cells from tissues. In normal cells, the negative phospholipids reside on the inner side of the cellular membrane while the outer surface of the membrane is occupied by uncharged phospholipids (PS). After a cell has entered apoptosis, the negatively charged PS are transported from the inner to the outer leaflet of the plasma membrane, thus exposing PS to the external cellular environment. The human anticoagulant, Annexin V, is a 35–36 kDa Ca²⁺-dependent phospholipid-binding protein that has a high affinity for PS. Annexin V labeled with a fluorophore or biotin can identify apoptotic cells by binding to PS exposed on the outer leaflet.

Propidium iodide (PI) is a membrane-impermeant DNA-binding dye that is commonly used to selectively stain dead cells in a cell population. PI is excluded by live cells and early apoptotic cells, but stains necrotic and late apoptotic cells with compromised membrane integrity. PI can be excited by the 488, 532, or 546 nm laser lines, and emits red fluorescence.

Based on Abbkine strong cell platform and advanced technology, Abbkine Annexin V Apoptosis Detection kits are generated at the right moment. Abbkine Annexin V Apoptosis Detection kit contains Annexin V labeled with Abbkine proprietary  AbFluor™ dyes, which allows the identification and quantitation of apoptotic cells by flow cytometry or fluorescence microscopy. Simultaneous staining of cells with AbFluor™ dyes and propidium iodide (PI) allows the discrimination of intact cells, early apoptotic and late apoptotic or necrotic cells.

Please see the below list for details

Product name	Cat#	Abs/Em
Annexin V-AbFluor™ 405 Apoptosis Detection kit	KTA0001	Annexin V- AbFluor™ 405: Abs/Em = 404/431 nm; PI: Abs/Em = 535/617 nm (with DNA)
Annexin V-AbFluor™ 488 Apoptosis Detection kit	KTA0002	Annexin V- AbFluor™ 488: Abs/Em = 491/517 nm; PI: Abs/Em = 535/617 nm (with DNA)
Annexin V-AbFluor™ 555 Apoptosis Detection kit	KTA0003	Annexin V- AbFluor™ 555: Abs/Em = 555/565 nm
Annexin V-AbFluor™ 647 Apoptosis Detection kit	KTA0004	Annexin V- AbFluor™ 555: Abs/Em = 555/565 nm; PI: Abs/Em = 535/617 nm (with DNA)

 

Abbkine offers a variety of Annexin V conjugates labeled with our outstanding series of AbFluor™ dyes. AbFluor™ dyes have equal or much better labeling performance than other fluorescent labeling dyes such as FITC, TRITC, Cy® dyes, Alexa Fluor® and Dylight® labeling dyes by having combined advantages in brightness, photostability, specificity and novel features ideal for in vivo imaging and flow cytometry.

Take Annexin V-AbFluor™ 488 Apoptosis Detection kit for example. The typical data is as below.

Hela cells were induced with camptothecin for 24 hours and stained with Annexin V- AbFluor™ 488 Apoptosis Detection Kit. The combination of AbFluor™ 488 and propidium iodide allows for the distinction between early apoptotic cells (Annexin V- AbFluor™ 488 positive), late apoptotic and/or necrotic cells (Annexin V- AbFluor™ 488 and propidium iodide positive), and viable cells (unstained).

 

Abbkine Scientific Co., Ltd.

Combining cutting edge technology from United States with China's manufacturing engineering and cost advantages, we aim to provide innovative, high quality assay kits, recombinant proteins, antibodies and other research tools to accelerate life science fundamental research, drug discovery, etc. Abbkine is aligned with, and responsive to, our customers’ ever-changing needs, making Abbkine a preferred discovery partner internationally.

A new research revealed that the CRISPR–Cas9 genome editing technique may increase cancer risk

Genome editing is a technology that genetic material can be added, removed, or altered at particular locations in the genome. CRISPR-Cas9 is short for clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9. This system is faster, cheaper, more accurate, and more efficient than other existing genome editing methods, so is popular with researchers.

CRISPR-Cas9 is a molecular machine first discovered in bacteria that can be programmed to go to an exact place in the genome, where it cuts the DNA. These precise 'molecular scissors' can be used to correct faulty pieces of DNA and are currently being used in clinical trials for cancer immunotherapy in the US and China. New trials are expected to be launched soon to treat inherited blood disorders such as sickle cell anemia.



Recently, a study entitled “CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response” was published in the journal of Nature Medicine, which found that therapeutic use of gene editing with CRISPR-Cas9 technique may inadvertently increase the risk of cancer. Researchers say that more studies are required to guarantee the safety of these 'molecular scissors' for gene-editing therapies.

In the study, genome editing by CRISPR–Cas9 induces a p53-mediated DNA damage response and cell cycle arrest in immortalized human retinal pigment epithelial cells, leading to a selection against cells with a functional p53 pathway. Inhibition of p53 prevents the damage response and increases the rate of homologous recombination from a donor template. These results suggest that p53 inhibition may improve the efficiency of genome editing of untransformed cells and that p53 function should be monitored when developing cell-based therapies utilizing CRISPR–Cas9.

Scientists from Karolinska Institutet and the University of Helsinki report that use of CRISPR-Cas9 in human cells in a laboratory setting can activate p53 protein, which acts as a cell's 'first aid kit' for DNA breaks. Once active, p53 reduces the efficiency of CRISPR-Cas9 gene editing. Thus, cells that do not have p53 or are unable to activate it show better gene editing. Unfortunately, however, lack of p53 is also known to contribute to making cells grow uncontrollably and become cancerous.

"By picking cells that have successfully repaired the damaged gene we intended to fix, we might inadvertently also pick cells without functional p53", says Dr Emma Haapaniemi, researcher and co-first author of the study. "If transplanted into a patient, as in gene therapy for inherited diseases, such cells could give rise to cancer, raising concerns for the safety of CRISPR-based gene therapies."

In conclusion, CRISPR-Cas9 is a powerful tool with staggering therapeutic potential, however, like all medical treatments, CRISPR-Cas9-based therapies might have side effects. The patients and caregivers should realize this point. Through the study, future work on the mechanisms that trigger p53 in response to CRISPR-Cas9 will be critical in improving the safety of CRISPR-Cas9-based therapies.

More information, please click https://ki.se/en/news/genome-editing-tool-could-increase-cancer-risk

Normal Donkey Serum Review

Normal serum is strongly recommended as a blocking reagent to reduce background from non-specific, conserved sequence and/or Fc receptor binding in Immunohistochemistry (IHC) or Immunofluorescence (IF) experiments. Normally, the species of blocking serum is the same as the host of secondary antibody.

Abbkine Normal Donkey Serum (Cat#BMS0140) was a new launched product in January, 2018.
Normal donkey serums, which are from non-immuned donkey hosts, are lipid extracted to improve clarity, dialyzed against phosphate buffered saline (PBS) containing sodium azide. Normal serum diluted to 5%-20% (v/v) in PBS is strongly recommended as a blocking reagent to reduce background from non-specific binding, or control for most immunoassay applications.

Features & Advantages

• High quality-Collect the blood from unimmunized normal adult hosts, then through lipid extracted and dialysis process, greatly avoiding the occurrence of hemolysis


• Wide application-IHC、ICC、IF、ELISA、BL


• Easy to use-Liquid package, directly diluted to PBS before use


• Good formulation-Reduced content of preservative, with less toxicity to cells/proteins


• Suggested application-Suggested starting dilutions are as follows: IHC-p (1:10-20), IF/ICC (1:10-20) and ELISA (1:100)

In four months, there already have two publications using Abbkine normal donkey serum.
1) Bone marrow mesenchymal stem cells protect against n-hexane-induced neuropathy through beclin 1-independent inhibition of autophagy. Hao J, Li S, Shi X, et al. Sci Rep, 2018, 8(1): 4516
2) 2,5-Hexanedione induces autophagic death of VSC41 cells via a PI3K/Akt/mTOR pathway. Guan H, Piao H, Qian Z et al. Mol Biosyst.

Please click Normal sera & IgGs to learn more Abbkine normal serum products.

Normal Donkey Serum Review

Normal serum is strongly recommended as a blocking reagent to reduce background from non-specific, conserved sequence and/or Fc receptor binding in Immunohistochemistry (IHC) or Immunofluorescence (IF) experiments. Normally, the species of blocking serum is the same as the host of secondary antibody.

Abbkine Normal Donkey Serum (Cat#BMS0140) was a new launched product in January, 2018.
Normal donkey serums, which are from non-immuned donkey hosts, are lipid extracted to improve clarity, dialyzed against phosphate buffered saline (PBS) containing sodium azide. Normal serum diluted to 5%-20% (v/v) in PBS is strongly recommended as a blocking reagent to reduce background from non-specific binding, or control for most immunoassay applications.

Features & Advantages

• High quality-Collect the blood from unimmunized normal adult hosts, then through lipid extracted and dialysis process, greatly avoiding the occurrence of hemolysis


• Wide application-IHC、ICC、IF、ELISA、BL


• Easy to use-Liquid package, directly diluted to PBS before use


• Good formulation-Reduced content of preservative, with less toxicity to cells/proteins


• Suggested application-Suggested starting dilutions are as follows: IHC-p (1:10-20), IF/ICC (1:10-20) and ELISA (1:100)

In four months, there already have two publications using Abbkine normal donkey serum.
1) Bone marrow mesenchymal stem cells protect against n-hexane-induced neuropathy through beclin 1-independent inhibition of autophagy. Hao J, Li S, Shi X, et al. Sci Rep, 2018, 8(1): 4516
2) 2,5-Hexanedione induces autophagic death of VSC41 cells via a PI3K/Akt/mTOR pathway. Guan H, Piao H, Qian Z et al. Mol Biosyst.

Please click Normal sera & IgGs to learn more Abbkine normal serum products.

The Nobel Prize in Physiology or Medicine 2017

The Nobel Prize in Physiology or Medicine 2017 was awarded jointly to Jeffrey C. Hall, Michael Rosbash and Michael W. Young "for their discoveries of molecular mechanisms controlling the circadian rhythm".

Nobelist	Born	Affiliation at the time of the award
Jeffrey C. Hall	1945, New York, NY, USA	University of Maine, Maine, ME, USA
Michael Rosbash	1944, Kansas City, MO, USA	Brandeis University, Waltham, MA, USA, Howard Hughes Medical Institute
Michael W. Young	1949, Miami, FL, USA	Rockefeller University, New York, NY, USA

Summary

Life on Earth is adapted to the rotation of our planet. For many years we have known that living organisms, including humans, have an internal, biological clock that helps them anticipate and adapt to the regular rhythm of the day. But how does this clock actually work? Jeffrey C. Hall, Michael Rosbash and Michael W. Young were able to peek inside our biological clock and elucidate its inner workings. Their discoveries explain how plants, animals and humans adapt their biological rhythm so that it is synchronized with the Earth's revolutions.

Using fruit flies as a model organism, this year's Nobel laureates isolated a gene that controls the normal daily biological rhythm. They showed that this gene encodes a protein that accumulates in the cell during the night, and is then degraded during the day. Subsequently, they identified additional protein components of this machinery, exposing the mechanism governing the self-sustaining clockwork inside the cell. We now recognize that biological clocks function by the same principles in cells of other multicellular organisms, including humans.

With exquisite precision, our inner clock adapts our physiology to the dramatically different phases of the day. The clock regulates critical functions such as behavior, hormone levels, sleep, body temperature and metabolism. Our wellbeing is affected when there is a temporary mismatch between our external environment and this internal biological clock, for example when we travel across several time zones and experience "jet lag". There are also indications that chronic misalignment between our lifestyle and the rhythm dictated by our inner timekeeper is associated with increased risk for various diseases.



More details, please click The 2017 Nobel Prize in Physiology or Medicine.

His Tag Antibodies ||| Abbkine

Abbkine provides unconjugated and conjugated with AbFluor™ 350, 405, 488, 555, 594, 647,680, Cy3, Cy5, FITC, HRP, Agarose, Magnetic Beads antibodies for your studying in the His Tag Antibodies research area.

[caption id="attachment_84014" align="aligncenter" width="412"] Immunofluorescence staining (1:2000) of HA fusion protein in 293 cells with red and counterstained with DAPI[/caption]

More product details, please click below links:

Quick links to His Tag Antibodies
Conjugate	Catalog no	Applications	Host
unconjugated	A02050	WB, IF, IP	Mouse
AbFluor™ 350	A02050A350	IF	Mouse
AbFluor™ 405	A02050A405	IF	Mouse
AbFluor™ 488	A02050A488	IF	Mouse
AbFluor™ 555	A02050A555	IF	Mouse
AbFluor™ 594	A02050A594	IF	Mouse
AbFluor™ 647	A02050A647	IF	Mouse
AbFluor™ 680	A02050A680	IF	Mouse
Cy3	A02050CY3	IF	Mouse
Cy5	A02050CY5	IF	Mouse
FITC	A02050FIT	IF	Mouse
Agarose	A02050AGB	IP	Mouse
Magnetic Beads	A02050MGB	IP	Mouse
unconjugated	A02051	WB	Rabbit
HRP	A02051HRP	WB	Rabbit
HRP	A02055	WB	Mouse
unconjugated	ABM40129	WB	Mouse
unconjugated	ABM40141	WB	Mouse
unconjugated	ABP50077	WB, ELISA	Rabbit

About Abbkine Scientific Co., Ltd.

Abbkine Scientific Co., Ltd. is a leading biotechnology company that focuses on developing and providing innovative, high quality assay kits, recombinant proteins, antibodies and other research tools to accelerate life science fundamental research, drug discovery, etc. Find more details, please visit the website at Abbkine.

His Tag Antibodies ||| Abbkine

Abbkine provides unconjugated and conjugated with AbFluor™ 350, 405, 488, 555, 594, 647,680, Cy3, Cy5, FITC, HRP, Agarose, Magnetic Beads antibodies for your studying in the His Tag Antibodies research area.

[caption id="attachment_84014" align="aligncenter" width="412"] Immunofluorescence staining (1:2000) of HA fusion protein in 293 cells with red and counterstained with DAPI[/caption]

More product details, please click below links:

Quick links to His Tag Antibodies
Conjugate	Catalog no	Applications	Host
unconjugated	A02050	WB, IF, IP	Mouse
AbFluor™ 350	A02050A350	IF	Mouse
AbFluor™ 405	A02050A405	IF	Mouse
AbFluor™ 488	A02050A488	IF	Mouse
AbFluor™ 555	A02050A555	IF	Mouse
AbFluor™ 594	A02050A594	IF	Mouse
AbFluor™ 647	A02050A647	IF	Mouse
AbFluor™ 680	A02050A680	IF	Mouse
Cy3	A02050CY3	IF	Mouse
Cy5	A02050CY5	IF	Mouse
FITC	A02050FIT	IF	Mouse
Agarose	A02050AGB	IP	Mouse
Magnetic Beads	A02050MGB	IP	Mouse
unconjugated	A02051	WB	Rabbit
HRP	A02051HRP	WB	Rabbit
HRP	A02055	WB	Mouse
unconjugated	ABM40129	WB	Mouse
unconjugated	ABM40141	WB	Mouse
unconjugated	ABP50077	WB, ELISA	Rabbit

About Abbkine Scientific Co., Ltd.

Abbkine Scientific Co., Ltd. is a leading biotechnology company that focuses on developing and providing innovative, high quality assay kits, recombinant proteins, antibodies and other research tools to accelerate life science fundamental research, drug discovery, etc. Find more details, please visit the website at Abbkine.

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Content introduction：

• A randomized trial of normothermic preservation in liver transplantation


• SAMHD1 acts at stalled replication forks to prevent interferon induction


• Renewing Felsenstein’s phylogenetic bootstrap in the era of big data


• Laser spectroscopic characterization of the nuclear-clock isomer ^229mTh


• Identification of the tumour transition states occurring during EMT

1. A randomized trial of normothermic preservation in liver transplantation

Liver transplantation is a highly successful treatment, but is severely limited by the shortage in donor organs. However, many potential donor organs cannot be used; this is because sub-optimal livers do not tolerate conventional cold storage and there is no reliable way to assess organ viability preoperatively. Normothermic machine perfusion maintains the liver in a physiological state, avoids cooling and allows recovery and functional testing. Here David Nasralla at University of Oxford in Oxford, UK and his colleagues show that, in a randomized trial with 220 liver transplantations, compared to conventional static cold storage, normothermic preservation is associated with a 50% lower level of graft injury, measured by hepatocellular enzyme release, despite a 50% lower rate of organ discard and a 54% longer mean preservation time. There was no significant difference in bile duct complications, graft survival or survival of the patient. If translated to clinical practice, these results would have a major impact on liver transplant outcomes and waiting list mortality.

Read more, please click https://www.nature.com/articles/s41586-018-0047-9

2. SAMHD1 acts at stalled replication forks to prevent interferon induction

SAMHD1 was previously characterized as a dNTPase that protects cells from viral infections. Mutations in SAMHD1 are implicated in cancer development and in a severe congenital inflammatory disease known as Aicardi–Goutières syndrome. The mechanism by which SAMHD1 protects against cancer and chronic inflammation is unknown. Here Flavie Coquel at University of Montpellier in Montpellier, France and his colleagues show that SAMHD1 promotes degradation of nascent DNA at stalled replication forks in human cell lines by stimulating the exonuclease activity of MRE11. This function activates the ATR–CHK1 checkpoint and allows the forks to restart replication. In SAMHD1-depleted cells, single-stranded DNA fragments are released from stalled forks and accumulate in the cytosol, where they activate the cGAS–STING pathway to induce expression of pro-inflammatory type I interferons. SAMHD1 is thus an important player in the replication stress response, which prevents chronic inflammation by limiting the release of single-stranded DNA from stalled replication forks.

Read more, please click https://www.nature.com/articles/s41586-018-0050-1

3. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Felsenstein’s application of the bootstrap method to evolutionary trees is one of the most cited scientific papers of all time. The bootstrap method, which is based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies based on hundreds or thousands of taxa are becoming routine. With phylogenies of this size Felsenstein’s bootstrap tends to yield very low supports, especially on deep branches. Here F. Lemoine at Institut Pasteur & CNRS in Paris, France and his colleagues propose a new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual ‘transfer’ distance rather than the binary presence or absence index used in Felsenstein’s original version. The resulting supports are higher and do not induce falsely supported branches. The application of their method to large mammal, HIV and simulated datasets reveals their phylogenetic signals, whereas Felsenstein’s bootstrap fails to do so.



Read more, please click https://www.nature.com/articles/s41586-018-0043-0

4. Laser spectroscopic characterization of the nuclear-clock isomer 229mTh

The isotope 229Th is the only nucleus known to possess an excited state 229mTh in the energy range of a few electronvolts—a transition energy typical for electrons in the valence shell of atoms, but about four orders of magnitude lower than typical nuclear excitation energies. Of the many applications that have been proposed for this nuclear system, which is accessible by optical methods, the most promising is a highly precise nuclear clock that outperforms existing atomic timekeepers. Here Johannes Thielking at Physikalisch-Technische Bundesanstalt in Braunschweig, Germany and his colleagues present the laser spectroscopic investigation of the hyperfine structure of the doubly charged 229mTh ion and the determination of the fundamental nuclear properties of the isomer, namely, its magnetic dipole and electric quadrupole moments, as well as its nuclear charge radius. Following the recent direct detection of this long-sought isomer, they provide detailed insight into its nuclear structure and present a method for its non-destructive optical detection.

Read more, please click https://www.nature.com/articles/s41586-018-0011-8

5. Identification of the tumour transition states occurring during EMT

In cancer, the epithelial-to-mesenchymal transition (EMT) is associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However, there is no direct in vivo evidence for this idea. Here Ievgenia Pastushenko at Université Libre de Buxelles in Brussels, Belgium and his colleagues screen a large panel of cell surface markers in skin and mammary primary tumours, and identify the existence of multiple tumour subpopulations associated with different EMT stages: from epithelial to completely mesenchymal states, passing through intermediate hybrid states. Although all EMT subpopulations presented similar tumour-propagating cell capacity, they displayed differences in cellular plasticity, invasiveness and metastatic potential. Their transcriptional and epigenetic landscapes identify the underlying gene regulatory networks, transcription factors and signalling pathways that control these different EMT transition states. Finally, these tumour subpopulations are localized in different niches that differentially regulate EMT transition states.

Read more, please click https://www.nature.com/articles/s41586-018-0040-3

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Content introduction：

• A randomized trial of normothermic preservation in liver transplantation


• SAMHD1 acts at stalled replication forks to prevent interferon induction


• Renewing Felsenstein’s phylogenetic bootstrap in the era of big data


• Laser spectroscopic characterization of the nuclear-clock isomer ^229mTh


• Identification of the tumour transition states occurring during EMT

1. A randomized trial of normothermic preservation in liver transplantation

Liver transplantation is a highly successful treatment, but is severely limited by the shortage in donor organs. However, many potential donor organs cannot be used; this is because sub-optimal livers do not tolerate conventional cold storage and there is no reliable way to assess organ viability preoperatively. Normothermic machine perfusion maintains the liver in a physiological state, avoids cooling and allows recovery and functional testing. Here David Nasralla at University of Oxford in Oxford, UK and his colleagues show that, in a randomized trial with 220 liver transplantations, compared to conventional static cold storage, normothermic preservation is associated with a 50% lower level of graft injury, measured by hepatocellular enzyme release, despite a 50% lower rate of organ discard and a 54% longer mean preservation time. There was no significant difference in bile duct complications, graft survival or survival of the patient. If translated to clinical practice, these results would have a major impact on liver transplant outcomes and waiting list mortality.

Read more, please click https://www.nature.com/articles/s41586-018-0047-9

2. SAMHD1 acts at stalled replication forks to prevent interferon induction

SAMHD1 was previously characterized as a dNTPase that protects cells from viral infections. Mutations in SAMHD1 are implicated in cancer development and in a severe congenital inflammatory disease known as Aicardi–Goutières syndrome. The mechanism by which SAMHD1 protects against cancer and chronic inflammation is unknown. Here Flavie Coquel at University of Montpellier in Montpellier, France and his colleagues show that SAMHD1 promotes degradation of nascent DNA at stalled replication forks in human cell lines by stimulating the exonuclease activity of MRE11. This function activates the ATR–CHK1 checkpoint and allows the forks to restart replication. In SAMHD1-depleted cells, single-stranded DNA fragments are released from stalled forks and accumulate in the cytosol, where they activate the cGAS–STING pathway to induce expression of pro-inflammatory type I interferons. SAMHD1 is thus an important player in the replication stress response, which prevents chronic inflammation by limiting the release of single-stranded DNA from stalled replication forks.

Read more, please click https://www.nature.com/articles/s41586-018-0050-1

3. Renewing Felsenstein’s phylogenetic bootstrap in the era of big data

Felsenstein’s application of the bootstrap method to evolutionary trees is one of the most cited scientific papers of all time. The bootstrap method, which is based on resampling and replications, is used extensively to assess the robustness of phylogenetic inferences. However, increasing numbers of sequences are now available for a wide variety of species, and phylogenies based on hundreds or thousands of taxa are becoming routine. With phylogenies of this size Felsenstein’s bootstrap tends to yield very low supports, especially on deep branches. Here F. Lemoine at Institut Pasteur & CNRS in Paris, France and his colleagues propose a new version of the phylogenetic bootstrap in which the presence of inferred branches in replications is measured using a gradual ‘transfer’ distance rather than the binary presence or absence index used in Felsenstein’s original version. The resulting supports are higher and do not induce falsely supported branches. The application of their method to large mammal, HIV and simulated datasets reveals their phylogenetic signals, whereas Felsenstein’s bootstrap fails to do so.



Read more, please click https://www.nature.com/articles/s41586-018-0043-0

4. Laser spectroscopic characterization of the nuclear-clock isomer 229mTh

The isotope 229Th is the only nucleus known to possess an excited state 229mTh in the energy range of a few electronvolts—a transition energy typical for electrons in the valence shell of atoms, but about four orders of magnitude lower than typical nuclear excitation energies. Of the many applications that have been proposed for this nuclear system, which is accessible by optical methods, the most promising is a highly precise nuclear clock that outperforms existing atomic timekeepers. Here Johannes Thielking at Physikalisch-Technische Bundesanstalt in Braunschweig, Germany and his colleagues present the laser spectroscopic investigation of the hyperfine structure of the doubly charged 229mTh ion and the determination of the fundamental nuclear properties of the isomer, namely, its magnetic dipole and electric quadrupole moments, as well as its nuclear charge radius. Following the recent direct detection of this long-sought isomer, they provide detailed insight into its nuclear structure and present a method for its non-destructive optical detection.

Read more, please click https://www.nature.com/articles/s41586-018-0011-8

5. Identification of the tumour transition states occurring during EMT

In cancer, the epithelial-to-mesenchymal transition (EMT) is associated with tumour stemness, metastasis and resistance to therapy. It has recently been proposed that, rather than being a binary process, EMT occurs through distinct intermediate states. However, there is no direct in vivo evidence for this idea. Here Ievgenia Pastushenko at Université Libre de Buxelles in Brussels, Belgium and his colleagues screen a large panel of cell surface markers in skin and mammary primary tumours, and identify the existence of multiple tumour subpopulations associated with different EMT stages: from epithelial to completely mesenchymal states, passing through intermediate hybrid states. Although all EMT subpopulations presented similar tumour-propagating cell capacity, they displayed differences in cellular plasticity, invasiveness and metastatic potential. Their transcriptional and epigenetic landscapes identify the underlying gene regulatory networks, transcription factors and signalling pathways that control these different EMT transition states. Finally, these tumour subpopulations are localized in different niches that differentially regulate EMT transition states.

Read more, please click https://www.nature.com/articles/s41586-018-0040-3