[Best evidence summary for awake prone positioning in treating hypoxemic due to COVID-19 infection]

Objective: To retrieve, evaluate, and summarize the best evidence for the treatment of hypoxemia in patients with COVID-19 infection using the awake prone positioning, with the aim of guiding healthcare professionals in the standardized implementation of this therapy. Methods: A systematic search was conducted in databases including UpToDate, BMJ Best Practice, JBI Evidence-Based Healthcare Center, American Association of Critical-Care Nurses, Intensive Care Society, European Respiratory Society, World Health Organization website, Cochrane Library, PubMed, China National Knowledge Infrastructure (CNKI), and Wanfang. The retrieved literature was subjected to quality assessment and evidence extraction. Results: A total of ten publications were included, consisting of one thematic evidence summary, one guideline, two systematic reviews, three randomized controlled trials, and three expert consensus statements. This summary synthesizes thirty key pieces of evidence in five categories: organizational management and training, risk assessment, preparatory operations, implementation key points, and risk control. Conclusions: Awake prone positioning is beneficial for improving hypoxemia in patients with COVID-19 and is easy to implement. Medical institutions should develop nursing management systems, operational standards, and best practices for awake prone positioning based on evidence-based evidence in order to improve the quality of care management for such patients.

[Research advances on size selection and vault prediction of posterior chamber phakic intraocular lens]

Posterior chamber phakic intraocular lens (pIOL) implantation has been widely adopted for the correction of refractive errors. Among pIOLs, the Implantable Collamer Lens is the most common choice. The selection of the appropriate pIOL size and achieving the desired postoperative vault to minimize complications has consistently been a focal point in academic research. With the advancement of ophthalmic biometric measurement technology and the application of artificial intelligence in the field of medicine, numerous new technologies and methods for pIOL size selection and vault prediction have emerged in recent years. This paper provides a comprehensive review on the topic of how to choose the pIOL size and predict the vault.

Large language models generate functional protein sequences across diverse families

Deep-learning language models have shown promise in various biotechnological applications, including protein design and engineering. Here we describe ProGen, a language model that can generate protein sequences with a predictable function across large protein families, akin to generating grammatically and semantically correct natural language sentences on diverse topics. The model was trained on 280 million protein sequences from >19,000 families and is augmented with control tags specifying protein properties. ProGen can be further fine-tuned to curated sequences and tags to improve controllable generation performance of proteins from families with sufficient homologous samples. Artificial proteins fine-tuned to five distinct lysozyme families showed similar catalytic efficiencies as natural lysozymes, with sequence identity to natural proteins as low as 31.4%. ProGen is readily adapted to diverse protein families, as we demonstrate with chorismate mutase and malate dehydrogenase.

[Association between anti-tissue transglutaminase antibody titers and duodenal histopathology among adults with celiac disease]

To evaluate the association between serum anti-tissue transglutaminase antibody (anti-tTG) titers and the severity of histological damage to the duodenal mucosa and to predict a possible anti-tTG cutoff value for diagnosing celiac disease (CD) and villous atrophy in the domestic population. Clinical and pathological data from 76 adult CD patients with positive anti-tTG titers and duodenal biopsy results who were treated at the People's Hospital of Xinjiang Uygur Autonomous Region from July 2017 to January 2022 were retrospectively analyzed. The correlation between anti-tTG titers and the severity of duodenal mucosal damage was statistically assessed to predict the optimal anti-tTG titer cut-off value for diagnosing CD and villous atrophy. Of the 76 patients, 10 had underlying CD, and of the 66 patients with duodenal histopathology, four were Marsh Ⅰ, six were Marsh Ⅱ, and 56 were Marsh Ⅲa-c grade. In adults with CD, anti-tTG titers were shown to be associated with the severity of histological damage to the duodenal mucosa. When the anti-tTG level was ≥5 times the upper limit of normal (ULN), the sensitivity and specificity for diagnosing CD were 83.9% and 92.9%, respectively. When the anti-tTG titer was ≥8 times the ULN, the sensitivity and specificity for diagnosing villous atrophy were 67.9% and 90.0%, respectively. Anti-tTG levels had a strong predictive value for diagnosing CD in adults when titers exceeded 10 times the ULN. Thus, the anti-tTG cut-off value can be combined with clinical judgment to diagnose CD, limiting the use of invasive endoscopy.

[The role of continuous 48 h oropharyngeal pH monitoring in the diagnosis of laryngopharyngeal reflux disease]

Objective: To investigate the daily variation of LPR and the significance of 48-hour oropharyngeal pH monitoring in the diagnosis of LPRD. Methods: 72 subjects with suspected LPRD who were treated in our department from June 2018 to June 2021 were included. All patients were hospitalized to complete continuous 48-hour oropharyngeal Dx-pH monitoring. The consistency of Ryan index and W index and the correlation of various reflux parameters between the first and second 24-hour were compared. SPSS 24.0 was used for statistical analysis. Results: All 72 subjects successfully completed 48-hour oropharyngeal Dx-pH monitoring. Ryan index was positive in 11 cases (15.2%) in the first 24-hour, in 17 cases (23.6%) in the second 24-hour, in 5 cases (6.9%) both first and second, and in 23 cases (31.9%) in either 24-hour, Kappa=0.211 (P=0.064), 18 cases (25%) had inconsistent results of the first 24-hour and the second 24-hour, and there was no significant difference in the positive rate between the first and second (P=0.234). The number of positive cases in 48-hour monitoring increased by 109.1% compared with 24-hour monitoring.For W index, 49 cases (68.1%) were positive in the first 24-hourf 53 cases (73.6%) were positive in the second 24-hour, 42 cases (58.3%) were positive both first and second, and 58 cases (80.6%) were positive in either 24-hour, Kappa=0.477 (P<0.001), 16 cases (22.2%) had inconsistent results of the first and second, and there was no significant difference in the positive rate between the first and second (P=0.804). The number of positive cases in 48-hour monitoring increased by 18.4% compared with 24-hour monitoring. There was no significant difference in all the reflux parameters of first and second (P>0.05). The correlation comparison showed that the correlation of various reflux parameters in the upright position was lower than that in the supine position. Conclusion: Laryngeal reflux has daily variability. Extending the monitoring time of Dx-pH to 48-hour can help reduce the missed diagnosis caused by daily variability; the use of W index can reduce the influence of daily variability on the diagnostic results of LPRD.

A MATLAB toolbox for modeling genetic circuits in cell-free systems

We introduce a MATLAB-based simulation toolbox, called txtlsim, for an Escherichia coli-based Transcription-Translation (TX-TL) system. This toolbox accounts for several cell-free-related phenomena, such as resource loading, consumption and degradation, and in doing so, models the dynamics of TX-TL reactions for the entire duration of solution phase batch-mode experiments. We use a Bayesian parameter inference approach to characterize the reaction rate parameters associated with the core transcription, translation and mRNA degradation mechanics of the toolbox, allowing it to reproduce constitutive mRNA and protein-expression trajectories. We demonstrate the use of this characterized toolbox in a circuit behavior prediction case study for an incoherent feed-forward loop.

Methodologies for preparation of prokaryotic extracts for cell-free expression systems

Cell-free systems that mimic essential cell functions, such as gene expression, have dramatically expanded in recent years, both in terms of applications and widespread adoption. Here we provide a review of cell-extract methods, with a specific focus on prokaryotic systems. Firstly, we describe the diversity of Escherichia coli genetic strains available and their corresponding utility. We then trace the history of cell-extract methodology over the past 20 years, showing key improvements that lower the entry level for new researchers. Next, we survey the rise of new prokaryotic cell-free systems, with associated methods, and the opportunities provided. Finally, we use this historical perspective to comment on the role of methodology improvements and highlight where further improvements may be possible.

[Dihydromyricin alleviates doxorubicin-induced myocardial injury by inhibiting NLRP3 inflammasome in rats]

Objective: To investigate the protective effect of dihydromyricetin (DHM) on doxorubicin (DOX)-induced myocardial injury and its mechanism. Methods: Twenty-four healthy male SD rats were divided into 4 groups: control group, DOX group, DOX+DHM100 group and DOX+DHM200 group. Echocardiography was used to measure cardiac function. At the end of the 6th week, the rats were anesthetized and sacrificed, and the pathological changes of the cardiac tissues were observed by HE staining, Masson staining and WGA staining. Cardiomyocyte apoptosis was observed by TUNEL staining, and protein levels of NLRP3, caspase-1, IL-1β, bax and bcl-2 were detected by Western blot and immunohistochemistry. Results: Compared with the control group, the left ventricular ejection fraction and left ventricular fractional shortening decreased significantly in DOX group, while left ventricular internal dimension at systole and left ventricular internal dimension at diastole increased. In DOX+DHM group, both left ventricular ejection fraction and left ventricular fractional shortening increased, while left ventricular internal dimension at systole and left ventricular internal dimension at diastole decreased (P<0.05). Furthermore, DOX group showed significant myocardial injury histologically, while DOX+DHM group significantly inhibited DOX-induced myocardial injury in rats. Meanwhile, cardiomyocyte hypertrophy was found in the DOX group, while the cardiomyocyte hypertrophy was notably inhibited in the DOX+DHM group. Compared with the control group, the apoptotic rates of cardiomyocytes and the levels of bax/bcl-2　ratio were significantly increased in DOX group, which were significantly alleviated in the DOX+DHM group (P<0.05). In addition, the levels of NLRP3, caspase-1 and IL-1β were increased as compared with control group, while the levels of the above indicators were remarkably reversed in DOX+DHM group as compared with DOX group (P<0.05). Conclusion: DHM alleviates DOX-induced myocardial injury in rats by inhibiting NLRP3 inflammasome and reducing cardiomyocyte apoptosis.

[The correlation between gastric bubble size and laryngopharyngeal reflux pattern in patients with laryngopharyngeal reflux disease]

Objective: To investigate the correlation between gastric bubble size and laryngopharyngeal reflux pattern in patients with laryngopharyngeal reflux disease(LPRD). Methods: A total of 52 LPRD patients who underwent Dx-pH monitoring and anteroposterior chest radiography at the same time from February 2016 to November 2018 were retrospectively studied. Patients were devided into three position-related groups according to the Ryan score of upright and supine: isolated upright reflux(IUR), isolated supine reflux(ISR) and bipositional reflux(BR) groups. In addition, 13 healthy volunteers with negative pH monitoring were selected as the control group. Gastric bubble size and pH monitoring data among the four groups were compared. SPSS 24.0 was used for statistical analysis. Results: In all the 52 patients, 35 cases (67.3%) were classified as IUR, 9 cases (17.3%) as ISR, and 8 cases (15.4%) as BR. The height of gastric bubbles in the four groups were: IUR (26±14) mm, ISR (9±8) mm, BR (20±13) mm, control (17±15) mm, and statistical difference was found among the four groups(P=0.004). Post Hoc Multiple Comparisons found that IUR group had statistical difference between ISR group and control group (P=0.001, P=0.034 respectively). There was no statistical difference of gastric bubble width and area among the four groups(P=0.340, P=0.186 respectively). The ROC curve of the gastric bubble height with isolated upright and supine reflux patterns was obtained, and the optimal cutoff value of the gastric bubble height was 11 mm. Accordingly, we divided the patiens into two groups with high and low gastric bubble. LPRD reflux pattern distribution was significantly different between the two groups(P<0.001). The comparison of reflux parameters in pH monitoring also showed that the supine reflux parameters in the lower group were significantly higher than those in the higher group, and the upright reflux parameters in the higher group were significantly higher than those in the lower group(P<0.001). Conclusions: The height of gastric bubble is significantly correlated with the reflux patterns in LPRD patients. The gastric bubble of patients with IUR is significantly higher than that of patients with ISR. Taking 11 mm as the cutoff value, patients with higher gastric bubble are more prone to upright laryngopharyngeal reflux, while those with lower gastric bubble are more prone to supine laryngopharyngeal reflux.

[Optic nerve morphology and vessel density in eyes with different phases of non-arteritic anterior ischemic optic neuropathy]

Objective: To compare the blood flow around the optic disc and related factors in patients with acute and chronic non-arteritic anterior ischemic optic neuropathy (NAION) and healthy volunteers with small disc cups under the same anatomical structure. Methods: This was a prospective case-control study. NAION patients with unilateral onset and healthy volunteers of the same phase were included in the study conducted at the Department of Ophthalmology of Peking Union Medical College Hospital between February 2017 and September 2018. Patients with a course of ≤ 3 months were categorized in the acute phase of NAION, and those with a course of >3 months were in the chronic phase of NAION. Healthy volunteers were in the control group. All subjects underwent the examination of best corrected visual acuity converted to logarithm of the minimum angle of resolution (LogMAR), measurement of non-contact intraocular pressure, slit lamp examination, small pupil fundus examination, and axial measurement. Optical coherence tomography was used to measure the thickness of retinal nerve fiber layers (RNFL) and retinal ganglion cell complex (GCC). Optical coherence tomography angiography was used to measure the vessel density around the optic disc. NAION patients underwent the visual field examination. Analysis of variance, non-parametric Mann-Whitney U test and Spearman coefficient was used for statistical analysis. Results: This study included 16 patients with acute phase of NAION, aged (57±9) years, 6 males and 10 females. There were 17 patients with chronic disease, aged (56±10) years, 7 males and 10 females. There were 15 healthy controls, aged (57±10) years old, 6 males and 9 females. There were no significant differences in age and gender between the groups (both P>0.05). The RNFL and the GCC in the NAION chronic phase group were significantly thinner than those in the acute phase group [(78±38) μm vs. (191±99) μm, (75±19) μm vs. (98±28) μm; t=4.389, 2.758; both P<0.05]. The cup/disc area ratio, cup/disc vertical diameter ratio and cup/disc horizontal diameter ratio in the chronic phase group were larger than those in the acute phase group [0.18 (0.11, 0.31) vs. 0.05 (0.01, 0.18), 0.45 (0.39, 0.56) vs. 0.22 (0.11, 0.41), 0.39 (0.28, 0.54) vs. 0.20 (0.07, 0.42)], and the difference was statistically significant (U=212.000, 208.000, 205.000; all P<0.05). Compared with the optic disc vessel density in the control group (53%±6%), there was a significant decrease in the acute phase group and the chronic phase group (45%±7%, 41%±8%; t=3.705, 4.940; both P<0.01). The blood vessel density in the nasal inferior of the chronic phase group was significantly lower than that in the acute phase group (36%±8% vs. 42%±7%, P=0.039), other sections didn't have significant difference (all P>0.05). There were tortuous capillaries in 8/16 of the acute phase cases, with a low blood flow density and visual field defect in relative positions. Correlation analysis showed that the whole density and peripapillary density in the NAION patients were negatively correlated with LogMAR, mean visual field defect, cup/disc area ratio, focal loss of volume of GCC and general loss of volume of GCC (r=-0.510, -0.733, -0.372, -0.532, -0.648; all P<0.01), but positively correlated with GCC and RNFL thickness (r=0.604, 0.508; both P<0.01). Conclusions: The optic disc vessel density in the acute phase and chronic phase of NAION is significantly reduced. The vessel density in the nasal area of the chronic phase is significantly reduced compared with the acute phase. The vessel density is correlated with visual acuity, visual field defect, disc indexes, thickness of RNFL and GCC. (Chin J Ophthalmol, 2019, 55: 677-686).

[Therapeutic effect of burr-hole operation combined with dural inversion and temporalis-periosteal synangiosis for ischemic moyamoya disease of adults]

Objective: To explore the therapeutic effect of burr-hole operation combined with dural inversion and temporalis-periosteal synangiosis for ischemic moyamoya disease of adults. Methods: The burr-hole operation combined with dural inversion and temporalis-periosteal synangiosis was performed on 21 adults with ischemic moyamoya disease since January 2013 in the second hospital of Shandong university.All of the patients were followed up for 3 months to 3 years.Digital subtraction angiogram (DSA) reexamination was performed and the cerebral MR perfusion imaging (PWI) was used to observe the perfusion of cerebral ischemic area before and after operation quantificationally, and the KPS scores before and after the surgery were analysed by the statistics.The clinical symptoms of the 21 patients gradually improved after the operation, there was statistical significance by paired t test of the KPS scores (P<0.001). Results: 19 patients were reexamined by DSA and PWI.The DSA results revealed there was apparent neovascularization in 65 burr-holes of total 72 holes , mainly came from the middle meningeal artery and superficial artery, and there was neovascularization in 33 burr-holes of total 35 holes whose arachnoid was completed, there was no statistical significance by χ(2) test (P>0.05). The revascularization of the ischemic cerebral tissue was obtained through the PWI.The postoperative complications included 1 case of subdural hematoma, 3 cases of postoperative temporary neurological deficits. Conclusion: The burr-hole operation combined with dural inversion and temporalis-periosteal synangiosis was effective, the MR perfusion imaging could assessment the effect exactly, there was no significant difference of neovascularization whether or not opening the arachnoid.

Percutaneous transforaminal endoscopic discectomy and miniincision surgery in the treatment of lumbar intervertebral disc protrusion

Lumbar intervertebral disc protrusion (LIDP) is a frequently occurring disease and 10-20% of patients require surgical treatment. Percutaneous transforaminal endoscopic discectomy (PTED) and mini-incision surgery are currently the most common surgeries for patients. To analyze the efficacy of PTED and mini-incision surgery in the treatment of lumbar intervertebral disc protrusion, this study selected 216 patients with LIDP who were admitted to the hospital between February 2014 and June 2015. The subjects were randomly divided into an observation group and a control group, 108 each. Patients in the observation groups were treated by PTED, while patients in the control group were treated by mini-incision surgery, and treatment efficacy of the two groups was observed. The results demonstrated that the duration of surgery and length of hospital stay of the observation group were significantly shorter than those of the control group, the intraoperative blood loss of the observation group was significantly less than that of the control group and the size of surgical incision of the observation group was much smaller than that of the control group (P less than 0.05). As to clinical efficacy, in accordance with the Japanese Orthopaedic Association (JOA) score and the Visual Analogue Scale (VAS) score, results of the observation group were superior to those of the control group at 3 months after surgery (P less than 0.05). In conclusion, treating patients with LIDP through PTED can significantly improve treatment efficacy, shorten surgical and healing time and relieve pain. This therapy is worth clinical promotion.

[Ryan index for detection of laryngopharyngeal reflux diseases]

Objective: To explore the utility of pharyngeal pH monitoring which positive standard is Ryan index in diagnosis of laryngopharyngeal reflux disease. Methods: In a retrospective study, clinical data of 590 patients who had symptoms laryngopharyngeal reflux disease from February 2016 to March 2017 were analyzed. All patients were received electronic laryngoscopy, assessment of reflux symptom index(RSI) and reflux finding score(RFS), and pharyngeal pH monitoring. SPSS 19.0 software was used to analyze the date. Results: There were 94 patients whose Ryan index were positive(15.93%). Among the 94 patients, 70 were positive during upright, 12 during supine and 12 during both upright and supine. There were 40 patients(6.78%)with pH decline events related to symptoms, while those Ryan index were normal. There were 536(90.85%), 417(70.68%), 233(39.49%) and 117(19.83%) patients with pH<6.5, pH<6.0, pH<5.5 and pH<5.0 events respectively. The positive rate of RSI, RFS, RSI and RFS, RSI or RFS were 44.24%, 16.78%, 7.12%, 53.90% respectively. The RFS score in Ryan index positive group was higher than that in Ryan index negative group[(8.2±2.4) vs (4.0±2.9), u=5.424, P<0.05], while the RSI score in Ryan index positive group was not statistically different from that in Ryan index negative group[(11.3±6.2) vs (12.7±5.8), t=1.247, P=0.167]. Conclusions: Pharyngeal pH monitoring is an objective and non-invasive method which can reflect laryngopharyngeal reflux directly. However, with the Ryan index as a criterion for the diagnosis of laryngopharyngeal reflux disease, partial patients may be missed. Further studies are needed to obtain more accurate and objective laryngopharyngeal pH statistical index for diagnosis of laryngopharyngeal reflux disease.

Rapid cell-free forward engineering of novel genetic ring oscillators

While complex dynamic biological networks control gene expression in all living organisms, the forward engineering of comparable synthetic networks remains challenging. The current paradigm of characterizing synthetic networks in cells results in lengthy design-build-test cycles, minimal data collection, and poor quantitative characterization. Cell-free systems are appealing alternative environments, but it remains questionable whether biological networks behave similarly in cell-free systems and in cells. We characterized in a cell-free system the ‘repressilator’, a three-node synthetic oscillator. We then engineered novel three, four, and five-gene ring architectures, from characterization of circuit components to rapid analysis of complete networks. When implemented in cells, our novel 3-node networks produced population-wide oscillations and 95% of 5-node oscillator cells oscillated for up to 72 hr. Oscillation periods in cells matched the cell-free system results for all networks tested. An alternate forward engineering paradigm using cell-free systems can thus accurately capture cellular behavior.

DOI:http://dx.doi.org/10.7554/eLife.09771.001

Engineers often use simplified models to test their ideas. For example, engineers test small-scale models of new airplane designs in wind tunnels to see how easily air flows by them. This saves the engineers the time and expense of building a full-sized aircraft only to learn it has serious design flaws.

The interactions of genes and proteins within living cells can be incredibly complex, and working out how a particular network works can take months or years in living cells. To try to speed up and simplify the process, scientists are developing models that do not involve cells. These models replicate the chemistry inside of the cells and allow scientists to observe complex interactions between genes, proteins and other cellular components. Some scientists have recreated complex patterns of gene expression in these cell-free models, but these systems still take a long time to make. It is also not yet clear whether these models accurately depict what happens in living cells.

Now, Niederholtmeyer, Sun et al. have created a cell-free system that allows the interactions of a large network of genes to be examined in a single day – a process that would previously have taken weeks or months. To test the model, Niederholtmeyer, Sun et al. recreated how networks of genes in the bacterium Escherichia coli interact to form “oscillations”, which produce a regular rhythm of gene expression. When the cell-free oscillator networks were inserted into live E. coli cells, the oscillators continued to produce the same patterns of gene expression as they did outside the cells.

Overall, the experiments show that cell-free models can accurately reproduce, or emulate, the behavior of cellular networks. This work now opens the door for engineering ever more complex genetic networks in a cell-free system, which in turn will enable rapid prototyping and detailed characterization of complex biological reaction networks.

DOI:http://dx.doi.org/10.7554/eLife.09771.002

Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems

RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on time scales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this potential is the slow design-build-test cycle of evaluating these networks in vivo. Here, we adapt an Escherichia coli-based cell-free transcription-translation (TX-TL) system for rapidly prototyping RNA networks. We used this system to measure the response time of an RNA transcription cascade to be approximately five minutes per step of the cascade. We also show that this response time can be adjusted with temperature and regulator threshold tuning. Finally, we use TX-TL to prototype a new RNA network, an RNA single input module, and show that this network temporally stages the expression of two genes in vivo.

Linear DNA for rapid prototyping of synthetic biological circuits in an Escherichia coli based TX-TL cell-free system

Accelerating the pace of synthetic biology experiments requires new approaches for rapid prototyping of circuits from individual DNA regulatory elements. However, current testing standards require days to weeks due to cloning and in vivo transformation. In this work, we first characterized methods to protect linear DNA strands from exonuclease degradation in an Escherichia coli based transcription-translation cell-free system (TX-TL), as well as mechanisms of degradation. This enabled the use of linear DNA PCR products in TX-TL. We then compared expression levels and binding dynamics of different promoters on linear DNA and plasmid DNA. We also demonstrated assembly technology to rapidly build circuits entirely in vitro from separate parts. Using this strategy, we prototyped a four component genetic switch in under 8 h entirely in vitro. Rapid in vitro assembly has future applications for prototyping multiple component circuits if combined with predictive computational models.

Seven novel MHC class I alleles identified in Cercopithecus mitis

We report here the identification of three Cemi-A and four Cemi-B novel alleles of Cercopithecus mitis.

Protocols for implementing an Escherichia coli based TX-TL cell-free expression system for synthetic biology

Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform.¹ This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology.^2,3 To achieve the latter goal, cell-free expression systems that preserve endogenous Escherichia coli transcription-translation mechanisms are able to more accurately reflect in vivo cellular dynamics than those based on T7 RNA polymerase transcription. We describe the preparation and execution of an efficient endogenous E. coli based transcription-translation (TX-TL) cell-free expression system that can produce equivalent amounts of protein as T7-based systems at a 98% cost reduction to similar commercial systems.^4,5 The preparation of buffers and crude cell extract are described, as well as the execution of a three tube TX-TL reaction. The entire protocol takes five days to prepare and yields enough material for up to 3000 single reactions in one preparation. Once prepared, each reaction takes under 8 hr from setup to data collection and analysis. Mechanisms of regulation and transcription exogenous to E. coli, such as lac/tet repressors and T7 RNA polymerase, can be supplemented.⁶ Endogenous properties, such as mRNA and DNA degradation rates, can also be adjusted.⁷ The TX-TL cell-free expression system has been demonstrated for large-scale circuit assembly, exploring biological phenomena, and expression of proteins under both T7- and endogenous promoters.^6,8 Accompanying mathematical models are available.^9,10 The resulting system has unique applications in synthetic biology as a prototyping environment, or "TX-TL biomolecular breadboard."

Immobilizing natural macromolecule on PLGA electrospun nanofiber with surface entrapment and entrapment-graft techniques

Surface entrapment is a convenient method to immobilize the natural macromolecules on the surface of synthetic polymers. In this study, the gelatin modified and sodium alginate/gelatin modified PLGA nanofibrous membranes were fabricated via surface entrapment and entrapment-graft techniques. The surface morphology of the each single modified PLGA nanofiber was as smooth as that of untreated PLGA nanofibers. The results of water angle contact measurements and tensile tests showed that the surface entrapment cannot only improve the hydrophilicity but also enhance mechanical properties of the modified nanofibrous membranes. In addition, the sodium alginate/gelatin modified electrospun PLGA nanofibrous membrane exhibited higher hydrophilicity and better biocompatibility than the simply gelatin modified PLGA nanofibrous membrane, which suggested the surface entrapment is a facile and efficient approach to surface modification for electrospun nanofibours membranes.

Fast domain wall propagation under an optimal field pulse in magnetic nanowires

We investigate field-driven domain wall (DW) propagation in magnetic nanowires in the framework of the Landau-Lifshitz-Gilbert equation. We propose a new strategy to speed up the DW motion in a uniaxial magnetic nanowire by using an optimal space-dependent field pulse synchronized with the DW propagation. Depending on the damping parameter, the DW velocity can be increased by about 2 orders of magnitude compared to the standard case of a static uniform field. Moreover, under the optimal field pulse, the change in total magnetic energy in the nanowire is proportional to the DW velocity, implying that rapid energy release is essential for fast DW propagation.

NFKB1-94ins/del polymorphism is not associated with lung injury after cardiopulmonary bypass

Nuclear factor (NF)-kappaB (NFKB1)-94ins/del is an important polymorphism that affects promoter activity of the NFKB1 gene and is potentially associated with several inflammatory diseases. We investigated the association of this polymorphism with lung injury after cardiac surgery and cardiopulmonary bypass in a prospective cohort study of 283 patients. Genotyping was performed by high resolution melting analysis; analysis indicated no association of NFKB1 with postoperative lung injury (p = 0.064). Relative risks of the del allele and the del/del genotype were 1.34 (95% CI 1.02-1.75) and 1.74 (95% CI 1.00-3.05) respectively. Logistic regression analysis (with factors including age, peripheral vascular disease and surgical duration as risk factors of lung injury after cardiac surgery with cardiopulmonary bypass) also failed to confirm that the NFKB1 genotype is influential for lung injury (p = 0.113). We conclude that, contrary to some other evidence, the NFKB1-94ins/del polymorphism is not associated with lung injury after cardiac surgery with cardiopulmonary bypass.

Programming cells by multiplex genome engineering and accelerated evolution

The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales. Although in vitro and directed evolution methods have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.

Theoretical limit in the magnetization reversal of stoner particles

Magnetization reversal of uniaxial Stoner particles under the Slonczewski spin-transfer torques of polarized electric currents is investigated. Based on the modified Landau-Lifshitz-Gilbert equation of magnetization dynamics, the theoretical limit of critical currents required to reverse a magnetization with an arbitrary polarized current is obtained. Under a constant polarization degree and constant current amplitude, the optimal current pulse for the fastest magnetization reversal is derived. These results can be used as benchmarks to evaluate different reversal strategies besides other possible usages.

Comparative analysis of cavity length-dependent temperature sensitivity of GaInNAs quantum dot lasers and quantum well lasers

Self-assembled GaInNAs/GaAsN single-layer quantum dot (QD) lasers, grown using solid source molecular beam epitaxy, have been fabricated and characterized. A high output power of 40.76 mW/facet was obtained from a GaInNAs QD laser with dimensions of 50 × 700 µm(2) at 10 °C. Temperature-dependent measurements were carried out on the GaInNAs QD lasers of different cavity lengths. For comparison, temperature-dependent measurements were also performed on GaInNAs single quantum well (SQW) and triple QW (TQW) lasers. Unlike the relationship between cavity length and T(0) in GaInNAs SQW/TQW lasers, longer-cavity GaInNAs QD lasers (50 × 1700 µm(2)) showed a lower T(0) of 65.1 K, which is believed to be due to non-uniformity of the GaInNAs QD layer. Furthermore, compared to GaInNAs SQW lasers, a significant improvement in temperature sensitivity was observed in the TQW GaInNAs lasers. This is attributed to a reduction in the relative contribution of the Auger recombination current and suppression of heavy-hole leakage in the TQW laser structures.

Theoretical limit of the minimal magnetization switching field and the optimal field pulse for Stoner particles

The theoretical limit of the minimal magnetization switching field and the optimal field pulse design for uniaxial Stoner particles are investigated. Two results are obtained. One is the existence of a theoretical limit of the smallest magnetic field out of all possible designs. It is shown that the limit is proportional to the damping constant in the weak damping regime and approaches the Stoner-Wohlfarth (SW) limit at large damping. For a realistic damping constant, this limit is more than 10 times smaller than that of so-called precessional magnetization reversal under a noncollinear static field. The other is on the optimal field pulse design: if the magnitude of a magnetic field does not change, but its direction can vary during a reversal process, there is an optimal design that gives the shortest switching time. The switching time depends on the field magnitude, damping constant, and magnetic anisotropy.

Self-assembled GaInNAs/GaAsN quantum dot lasers: solid source molecular beam epitaxy growth and high-temperature operation

Self-assembled GaInNAs quantum dots (QDs) were grown on GaAs (001) substrate using solid-source molecular-beam epitaxy (SSMBE) equipped with a radio-frequency nitrogen plasma source. The GaInNAs QD growth characteristics were extensively investigated using atomic-force microscopy (AFM), photoluminescence (PL), and transmission electron microscopy (TEM) measurements. Self-assembled GaInNAs/GaAsN single layer QD lasers grown using SSMBE have been fabricated and characterized. The laser worked under continuous wave (CW) operation at room temperature (RT) with emission wavelength of 1175.86 nm. Temperature-dependent measurements have been carried out on the GaInNAs QD lasers. The lowest obtained threshold current density in this work is ∼1.05 kA/cm²from a GaInNAs QD laser (50 × 1,700 µm²) at 10 °C. High-temperature operation up to 65 °C was demonstrated from an unbonded GaInNAs QD laser (50 × 1,060 µm²), with high characteristic temperature of 79.4 K in the temperature range of 10–60 °C.

Identification of differentially transcribed genes in human lymphoblastoid cells irradiated with 0.5 Gy of gamma-ray and the involvement of low dose radiation inducible CHD6 gene in cell proliferation and radiosensitivity

PURPOSE

To identify candidate genes specifically involved in response to low-dose irradiation in human lymphoblastoid cells; to better clarify the role of the human chromodomain helicase DNA binding protein 6 gene (CHD6), one of these genes, in cell proliferation and radiosensitivity.

MATERIALS AND METHODS

DNA microarray technology was used to analyse global transcriptional profile in human lymphoblastoid AHH-1 cells at 4 h after exposure to 0.5 Gy of gamma-ray. Gene expression changes were confirmed by semi-quantitative reverse transcription--polymerase chain reaction (RT-PCR) and Northern blot. RNA interfering technology was employed to knock-down the CHD6 gene in A549 cells. Colony-forming ability was used to analyse radiosensitivity.

RESULTS

The microarray assay revealed a set of 0.5 Gy-responsive genes, including 30 up-regulated genes and 45 down-regulated genes. The up-regulated genes include a number of genes involved in: signal transduction pathways, e.g., STAT3, CAMKK2, SIRT1, CREM, MAPK3K7IP2 and GPR56; transcription or DNA-binding, e.g., CHD6, CRSP3, SNURF, SH2 domain binding protein 1 and MIZF. Some of the down-regulated genes are involved in: cytoskeleton and cell movement (WASF2, LCP1, MSN, NIPSNAP1, KIF2C); DNA replication and repair (MCM2, MCM3, MCM7 and XRCC-4). Radiation-increased expression of CHD6 was also found in A549 cells and HeLa cells. The sustained CHD6 induction was restricted to relatively low doses (0.2 Gy or 0.5 Gy), no change occurring after 4 Gy irradiation. Silencing of CHD6 mediated by siRNA increased the growth rate of A549 cells by 40 approximately 60%. Most importantly, silencing CHD6 led to an increased radioresistance of A459 cells to radiation doses up to 2 Gy, but barely affected the sensitivity of cells at 4 and 8 Gy.

CONCLUSION

This study has identified a set of genes responsive to 0.5 Gy of gamma-rays. CDH6 gene can be specifically up-regulated by low dose irradiation, and its inducible expression could be involved in a low dose hypersensitive response.

Histological type and syncytial growth pattern affect E-cadherin expression in a multifactorial analysis of a combined panel of sporadic and BRCA1-associated breast cancers

E-cadherin is a prominent factor in maintaining the epithelial architecture, and loss of its normal function is considered to be a key element in cancer invasion. In breast cancer, correlation between alteration of E-cadherin expression and histological type has been reported, but associations with other parameters remain uncertain. To refine these findings and to explore the biological significance of features thought to result from alterations of cell-to-cell adhesion systems, rare in sporadic cases but more frequent in BRCA1-associated breast cancers (BRCA1-BCs), we investigated E-cadherin expression by immuno-histochemistry in a combined panel of 214 breast cancers enriched in hereditary cases (176 sporadic cases and 38 BRCA1-BCs). Following multivariate statistical analysis using a logistic regression model, only 2 parameters were significantly associated with loss of E-cadherin expression: lobular histological type (p < 0.0001), in agreement with previous results, and syncytial growth pattern (SGP) (p = 0.01). The latter result provides a biological basis for SGP, the cardinal feature of medullary breast carcinoma.

FGF7 protein expression in human breast carcinomas

FGFs, especially FGF7, are thought to play an important role in the stroma-epithelium interactions that take place in several tissues, including the prostate and mammary glands. Using an immunohistochemistry approach, FGF7 protein expression was measured in a series of 80 human breast carcinomas. FGF7 was found to be expressed in two-thirds of cases studied, either in the stroma or in the tumour cells. Although it did not reach significance level, a tendency was noted for FGF7 expression to be associated with the most differentiated and least aggressive tumours.

Angiogenesis as a prognostic marker in breast carcinoma with conventional adjuvant chemotherapy: a multiparametric and immunohistochemical analysis

It has now been clearly established that quantitative immunohistochemical methods applied to tumour angiogenesis under suitable quality control conditions are a powerful prognostic tool for use in the initial assessment of breast carcinomas. Appropriate parameters for predicting the aggressiveness of tumours and their sensitivity to treatment are, however, still required. To determine whether the microvessel count (MVC) may serve to predict the chemotherapeutic response, a retrospective study was carried out on a series of 162 patients with breast carcinoma, who were all treated with the same standard adjuvant chemotherapy. Angiogenesis was assessed by performing CD31 immunostaining and MVC per mm2. Several other factors such as P53, ERBB2, BCL2, and Ki67 were also measured, and their prognostic value was compared with that of the MVC. The MVC was not found to be correlated with any of the other prognostic parameters, but turned out to be of great prognostic value whatever the threshold value chosen, which suggests that it is continuously valid at all levels. The median value of the MVC (43.5 per mm2) divided this series into two significantly different prognostic categories, in terms of both disease-free survival (P = 0.0002) and overall survival (P = 0.037). Univariate analysis showed that most of the parameters analysed were of prognostic value regarding the disease-free survival, namely grade (P = 0.029), mitotic index (P = 0.049), size (P = 0.015), oestrogen receptors (P = 0.022), progesterone receptors (P = 0.018), P53 (P = 0.0045), ERBB2 (P = 0.046), and Ki67 (P = 0.0008). As regards overall survival, grade and ERBB2 showed a loss of prognostic value. In multivariate analysis on disease-free survival, the MVC was the most accurate prognostic factor (RR = 2.64), followed by Ki67 (RR = 2.06) and P53 (RR = 1.69). With respect to overall survival, the MVC ranked third among the prognostic parameters analysed. Standard chemotherapy did not reduce the high prognostic value of the MVC performed on tumour angiogenesis. This suggests that the MVC may predict the degree of resistance to chemotherapy. Patients with high levels of angiogenesis, particularly node-negative patients, might therefore be able to benefit from adjuvant therapy of another kind.