A flexible, modular and versatile functional part assembly toolkit for gene cluster engineering in Streptomyces

Streptomyces has enormous potential to produce novel natural products (NPs) as it harbors a huge reservoir of uncharacterized and silent natural product biosynthetic gene clusters (BGCs). However, the lack of efficient gene cluster engineering strategies has hampered the pace of new drug discovery. Here, we developed an easy-to-use, highly flexible DNA assembly toolkit for gene cluster engineering. The DNA assembly toolkit is compatible with various DNA assembling approaches including Biobrick, Golden Gate, CATCH, yeast homologous recombination-based DNA assembly and homing endonuclease-mediated assembly. This compatibility offers great flexibility in handling multiple genetic parts or refactoring large gene clusters. To demonstrate the utility of this toolkit, we quantified a library of modular regulatory parts, and engineered a gene cluster (act) using characterized promoters that led to increased production. Overall, this work provides a powerful part assembly toolkit that can be used for natural product discovery and optimization in Streptomyces.

Corrigendum to "Improving cooperativity of transcription activators by oligomerization domains in mammalian cells" [Synth Syst Biotechnol 8 (1) (2023) 114-120]

[This corrects the article DOI: 10.1016/j.synbio.2022.12.003.].

Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system

Context-dependency of mammalian transcriptional elements has hindered the quantitative investigation of multigene expression stoichiometry and its biological functions. Here, we describe a host- and local DNA context-independent transcription system to gradually fine-tune single and multiple gene expression with predictable stoichiometries. The mammalian transcription system is composed of a library of modular and programmable promoters from bacteriophage and its cognate RNA polymerase (RNAP) fused to a capping enzyme. The relative expression of single genes is quantitatively determined by the relative binding affinity of the RNAP to the promoters, while multigene expression stoichiometry is predicted by a simple biochemical model with resource competition. We use these programmable and modular promoters to predictably tune the expression of three components of an influenza A virus-like particle (VLP). Optimized stoichiometry leads to a 2-fold yield of intact VLP complexes. The host-independent orthogonal transcription system provides a platform for dose-dependent control of multiple protein expression which may be applied for advanced vaccine engineering, cell-fate programming and other therapeutic applications.

Improving cooperativity of transcription activators by oligomerization domains in mammalian cells

Cooperative activation is critical for the applications of synthetic biology in mammalian cells. In this study, we have developed cooperative transcription factor by fusing oligomerization domain in mammalian cells. Firstly, we demonstrated that two oligomerized domains (CI434 and CI) successfully improved transcription factor cooperativity in bacterial cells but failed to increase cooperativity in mammalian cells, possibly because the additional mammalian activation domain disrupted their oligomerization capability. Therefore, we chose a different type of oligomerized domain (CarHC), whose ability to oligomerize is not dependent on its C-terminal domains, to fuse with a transcription factor (RpaR) and activation domain (VTR3), forming a potential cooperative transcription activator RpaR-CarH-VTR3 for mammalian regulatory systems. Compared with RpaR-VTR3, the cooperativity of RpaR-CarH-VTR3 was significantly improved with higher Hill coefficient and a narrower input range in the inducible switch system in mammalian cells. Moreover, a mathematical model based on statistical mechanics model was developed and the simulation results supported the hypothesis that the tetramer of the CarH domain in mammalian cells was the reason for the cooperative capacity of RpaR-CarH-VTR3.

The Topological Characteristics of Biological Ratio-Sensing Networks

Ratio sensing is a fundamental biological function observed in signal transduction and decision making. In the synthetic biology context, ratio sensing presents one of the elementary functions for cellular multi-signal computation. To investigate the mechanism of the ratio-sensing behavior, we explored the topological characteristics of biological ratio-sensing networks. With exhaustive enumeration of three-node enzymatic and transcriptional regulatory networks, we found that robust ratio sensing was highly dependent on network structure rather than network complexity. Specifically, a set of seven minimal core topological structures and four motifs were deduced to be capable of robust ratio sensing. Further investigations on the evolutionary space of robust ratio-sensing networks revealed highly clustered domains surrounding the core motifs which suggested their evolutionary plausibility. Our study revealed the network topological design principles of ratio-sensing behavior and provided a design scheme for constructing regulatory circuits with ratio-sensing behavior in synthetic biology.

Paired dCas9 design as a nucleic acid detection platform for pathogenic strains

The wide application of molecular beacon probes in specific DNA detection, especially in the fast prototyping of pathogen DNA detection kits in point-of-care diagnostics, has been hindered by the nonflexible choice of target sequences and the unstable fluorophore output. We developed an in vitro DNA detection system consisting of a pair of dCas9 proteins linked to split halves of luciferase, named the Paired dCas9 (PC) reporter. Co-localization of the reporter pair to a ~46 bp target sequence defined by two single guide RNAs (sgRNAs) activated luciferase which subsequently generated highly intensified luminescent signals. Combined with an array design and statistical analyses, the PC reporter system could be programmed to access sequence information across the entire genome of the pathogenic Mycobacterium tuberculosis H37Rv strain. These findings suggest great potential for the PC reporter in effective and affordable in vitro nucleic acid detection technologies. In this article we highlighted the systems design from our previous researchworkon the PC reporter (Zhang et al, 2015)with a focuson methodology.

Mitigating Host Burden of Genetic Circuits by Engineering Autonegatively Regulated Parts and Improving Functional Prediction

Mitigating unintended interferences between circuits and host cells is key to realize applications of synthetic regulatory systems both for bacteria and mammalian cells. Here, we demonstrated that growth burden and circuit dysregulation occurred in a concentration-dependent manner for specific transcription factors (CymR*/CymR) in E.coli, and direct negative feedback modules were able to control the concentration of CymR*/CymR, mitigate growth burden, and restore circuit functions. A quantitative design scheme was developed for circuits embedded with autorepression modules. Four key parameters were theoretically identified to determine the performance of autoregulated switches and were experimentally modified by fine-tuning promoter architectures and cooperativity. Using this strategy, we synthesized a number of switches and demonstrated its improvement of product titers and host growth controlling the complex deoxyviolacein biosynthesis pathway. Furthermore, we restored functions of a dysregulated multilayer NOR gate by integrating autorepression modules. Our work provides a blueprint for engineering host-adaptable synthetic systems.

Multiplexed Promoter Engineering for Improving Thaxtomin A Production in Heterologous Streptomyces Hosts

Thaxtomin A is a potent bioherbicide in both organic and conventional agriculture; however, its low yield hinders its wide application. Here, we report the direct cloning and heterologous expression of the thaxtomin A gene cluster in three well-characterized Streptomyces hosts. Then, we present an efficient, markerless and multiplex large gene cluster editing method based on in vitro CRISPR/Cas9 digestion and yeast homologous recombination. With this method, we successfully engineered the thaxtomin A cluster by simultaneously replacing the native promoters of the txtED operon, txtABH operon and txtC gene with strong constitutive promoters, and the yield of thaxtomin A improved to 289.5 µg/mL in heterologous Streptomyces coelicolor M1154. To further optimize the biosynthetic pathway, we used constraint-based combinatorial design to build 27 refactored gene clusters by varying the promoter strength of every operon, and the highest titer of thaxtomin A production reached 504.6 μg/mL. Taken altogether, this work puts forward a multiplexed promoter engineering strategy to engineer secondary metabolism gene clusters for efficiently improving fermentation titers.

Synthetic robust perfect adaptation achieved by negative feedback coupling with linear weak positive feedback

Unlike their natural counterparts, synthetic genetic circuits are usually fragile in the face of environmental perturbations and genetic mutations. Several theoretical robust genetic circuits have been designed, but their performance under real-world conditions has not yet been carefully evaluated. Here, we designed and synthesized a new robust perfect adaptation circuit composed of two-node negative feedback coupling with linear positive feedback on the buffer node. As a key feature, the linear positive feedback was fine-tuned to evaluate its necessity. We found that the desired function was robustly achieved when genetic parameters were varied by systematically perturbing all interacting parts within the topology, and the necessity of the completeness of the topological structures was evaluated by destroying key circuit features. Furthermore, different environmental perturbances were imposed onto the circuit by changing growth rates, carbon metabolic strategies and even chassis cells, and the designed perfect adaptation function was still achieved under all conditions. The successful design of a robust perfect adaptation circuit indicated that the top-down design strategy is capable of predictably guiding bottom-up engineering for robust genetic circuits. This robust adaptation circuit could be integrated as a motif into more complex circuits to robustly implement more sophisticated and critical biological functions.

Engineered DNase-inactive Cpf1 variants to improve targeting scope for base editing in E. coli

The development of base editing (BE) technology has opened a new avenue for research studies in bacteriology, particularly for bacterial species in which the DNA double-strand breaks (DSBs) introduced by CRISPR/Cas system would lead to cell death. However, a major limitation of BE-mediated gene editing is the restricted editable sites in the target bacterial genome due to highly diverse genomic compositions, such as GC content. Herein, we developed a broad-spectrum DNase-inactive Cpf1 (dCpf1) variant from Francisella novicida (bsdFnCpf1) through directed evolution. The resulting optimized mutant showed a substantially expanded targeting range, including previously non-canonical protospacer-adjacent motifs (PAMs), especially the GC-rich PAMs. Cytidine deaminase APOBEC1 and uracil DNA glycosylase inhibitor (UGI) were fused with bsdFnCpf1 to achieve specific C to T mutations at multiple target sites with canonical or non-canonical PAMs in the E. coli genome without compromising cell growth. We anticipate that bsdFnCpf1 could be applied for multiplex gene regulation and BE in species that have been reported to be suitable for Cpf1.

De novo design of an intercellular signaling toolbox for multi-channel cell-cell communication and biological computation

Intercellular signaling is indispensable for single cells to form complex biological structures, such as biofilms, tissues and organs. The genetic tools available for engineering intercellular signaling, however, are quite limited. Here we exploit the chemical diversity of biological small molecules to de novo design a genetic toolbox for high-performance, multi-channel cell-cell communications and biological computations. By biosynthetic pathway design for signal molecules, rational engineering of sensing promoters and directed evolution of sensing transcription factors, we obtain six cell-cell signaling channels in bacteria with orthogonality far exceeding the conventional quorum sensing systems and successfully transfer some of them into yeast and human cells. For demonstration, they are applied in cell consortia to generate bacterial colony-patterns using up to four signaling channels simultaneously and to implement distributed bio-computation containing seven different strains as basic units. This intercellular signaling toolbox paves the way for engineering complex multicellularity including artificial ecosystems and smart tissues.

A tight cold-inducible switch built by coupling thermosensitive transcriptional and proteolytic regulatory parts

Natural organisms have evolved intricate regulatory mechanisms that sense and respond to fluctuating environmental temperatures in a heat- or cold-inducible fashion. Unlike dominant heat-inducible switches, very few cold-inducible genetic switches are available in either natural or engineered systems. Moreover, the available cold-inducible switches still have many shortcomings, including high leaky gene expression, small dynamic range (<10-fold) or broad transition temperature (>10°C). To address these problems, a high-performance cold-inducible switch that can tightly control target gene expression is highly desired. Here, we introduce a tight and fast cold-inducible switch that couples two evolved thermosensitive variants, TF_ts and TEV_ts, as well as an additional Mycoplasma florum Lon protease (mf-Lon) to effectively turn-off target gene expression via transcriptional and proteolytic mechanisms. We validated the function of the switch in different culture media and various Escherichia coli strains and demonstrated its tightness by regulating two morphogenetic bacterial genes and expressing three heat-unstable recombinant proteins, respectively. Moreover, the additional protease module enabled the cold-inducible switch to actively remove the pre-existing proteins in slow-growing cells. This work establishes a high-performance cold-inducible system for tight and fast control of gene expression which has great potential for basic research, as well as industrial and biomedical applications.

A Direct RNA-to-RNA Replication System for Enhanced Gene Expression in Bacteria

A long-standing objective of metabolic engineering has been to exogenously increase the expression of target genes. In this research, we proposed the permanent RNA replication system using DNA as a template to store genetic information in bacteria. We selected Qβ phage as the RNA replication prototype and made many improvements to achieve target gene expression enhancement directly by increasing mRNA abundance. First, we identified the endogenous gene Rnc, the knockout of which significantly improved the RNA replication efficiency. Second, we elucidated the essential elements for RNA replication and optimized the system to make it more easily applicable. Combined with optimization of the host cell and the system itself, we developed a stable RNA-to-RNA replication tool to directly increase the abundance of the target mRNA and subsequently the target protein. Furthermore, it was proven efficient in enhancing the expression of specific proteins and was demonstrated to be applicable in metabolic engineering. Our system has the potential to be combined with any of the existing methods for increasing gene expression.

Oromandibular reconstruction using microvascularized bone flap: report of 1038 cases from a single institution

This retrospective study was performed to review 1038 patients who underwent mandibular reconstruction with free vascularized bone flaps at a single institution between 2006 and 2017. Of these patients, 827 (79.67%) had fibula flaps, 197 (18.98%) had deep circumflex iliac artery perforator (DCIA) flaps, and 11 (1.06%) had scapula bone flaps. The most common pathological diagnosis was ameloblastoma (n=366, 35.26%), followed by squamous cell carcinoma (n=278, 26.78%) and osteoradionecrosis (n=152, 14.64%). Fifty-seven patients (5.49%) had major complications requiring surgical intervention and one patient died of a pulmonary embolism. Venous crisis was the most frequent major complication (n=20, 1.93%), followed by haematoma (n=17, 1.64%) and flap necrosis (n=14, 1.35%). One-stage mandibular reconstruction was preferred whenever possible, as this generally decreases the financial and hospitalization burden. The four-segment method of jaw reconstruction appeared to achieve good aesthetic appearance results in Asian patients and this was not associated with a higher risk of segment ischemia compared with the three-segment method.

Systematically investigating the key features of the DNase deactivated Cpf1 for tunable transcription regulation in prokaryotic cells

With a unique crRNA processing capability, the CRISPR associated Cpf1 protein holds great potential for multiplex gene regulation. Unlike the well-studied Cas9 protein, however, conversion of Cpf1 to a transcription regulator and its related properties have not been systematically explored yet. In this study, we investigated the mutation schemes and crRNA requirements for the DNase deactivated Cpf1 (dCpf1). By shortening the direct repeat sequence, we obtained genetically stable crRNA co-transcripts and improved gene repression with multiplex targeting. A screen of diversity-enriched PAM library was designed to investigate the PAM-dependency of gene regulation by dCpf1 from Francisella novicida and Lachnospiraceae bacterium. We found novel PAM patterns that elicited strong or medium gene repressions. Using a computational algorithm, we predicted regulatory outputs for all possible PAM sequences, which spanned a large dynamic range that could be leveraged for regulatory purposes. These newly identified features will facilitate the efficient design of CRISPR-dCpf1 based systems for tunable multiplex gene regulation.

A genetically engineered Escherichia coli that senses and degrades tetracycline antibiotic residue

Due to the abuse of antibiotics, antibiotic residues can be detected in both natural environment and various industrial products, posing threat to the environment and human health. Here we describe the design and implementation of an engineered Escherichia coli capable of degrading tetracycline (Tc)-one of the commonly used antibiotics once on humans and now on poultry, cattle and fisheries. A Tc-degrading enzyme, TetX, from the obligate anaerobe Bacteroides fragilis was cloned and recombinantly expressed in E. coli and fully characterized, including its K m and k cat value. We quantitatively evaluated its activity both in vitro and in vivo by UV-Vis spectrometer and LC-MS. Moreover, we used a tetracycline inducible amplification circuit including T7 RNA polymerase and its specific promoter PT7 to enhance the expression level of TetX, and studied the dose-response of TetX under different inducer concentrations. Since the deployment of genetically modified organisms (GMOs) outside laboratory brings about safety concerns, it is necessary to explore the possibility of integrating a kill-switch. Toxin-Antitoxin (TA) systems were used to construct a mutually dependent host-plasmid platform and biocontainment systems in various academic and industrious situations. We selected nine TA systems from various bacteria strains and measured the toxicity of toxins (T) and the detoxifying activity of cognate antitoxins (A) to validate their potential to be used to build a kill-switch. These results prove the possibility of using engineered microorganisms to tackle antibiotic residues in environment efficiently and safely.

Engineering the Ultrasensitive Transcription Factors by Fusing a Modular Oligomerization Domain

The dimerization and high-order oligomerization of transcription factors has endowed them with cooperative regulatory capabilities that play important roles in many cellular functions. However, such advanced regulatory capabilities have not been fully exploited in synthetic biology and genetic engineering. Here, we engineered a C-terminally fused oligomerization domain to improve the cooperativity of transcription factors. First, we found that two of three designed oligomerization domains significantly increased the cooperativity and ultrasensitivity of a transcription factor for the regulated promoter. Then, seven additional transcription factors were used to assess the modularity of the oligomerization domains, and their ultrasensitivity was generally improved, as assessed by their Hill coefficients. Moreover, we also demonstrated that the allosteric capability of the ligand-responsive domain remained intact when fusing with the designed oligomerization domain. As an example application, we showed that the engineered ultrasensitive transcription factor could be used to significantly improve the performance of a "stripe-forming" gene circuit. We envision that the oligomerization modules engineered in this study could act as a powerful tool to rapidly tune the underlying response profiles of synthetic gene circuits and metabolic pathway controllers.

Orthogonality and Burdens of Heterologous AND Gate Gene Circuits in E. coli

Synthetic biology approaches commonly introduce heterologous gene networks into a host to predictably program cells, with the expectation of the synthetic network being orthogonal to the host background. However, introduced circuits may interfere with the host’s physiology, either indirectly by posing a metabolic burden and/or through unintended direct interactions between parts of the circuit with those of the host, affecting functionality. Here we used RNA-Seq transcriptome analysis to quantify the interactions between a representative heterologous AND gate circuit and the host Escherichia coli under various conditions including circuit designs and plasmid copy numbers. We show that the circuit plasmid copy number outweighs circuit composition for their effect on host gene expression with medium-copy number plasmid showing more prominent interference than its low-copy number counterpart. In contrast, the circuits have a stronger influence on the host growth with a metabolic load increasing with the copy number of the circuits. Notably, we show that variation of copy number, an increase from low to medium copy, caused different types of change observed in the behavior of components in the AND gate circuit leading to the unbalance of the two gate-inputs and thus counterintuitive output attenuation. The study demonstrates the circuit plasmid copy number is a key factor that can dramatically affect the orthogonality, burden and functionality of the heterologous circuits in the host chassis. The results provide important guidance for future efforts to design orthogonal and robust gene circuits with minimal unwanted interaction and burden to their host.

MiR-128 regulation of glucose metabolism and cell proliferation in triple-negative breast cancer

BACKGROUND

Triple-negative breast cancer (TNBC) is prone to metastasis and has a poor prognosis, with lower survival rates than other breast cancer subtypes. MicroRNAs have recently emerged as powerful regulators of cancer processes and become a promising target in cancer therapy.

METHODS

Expression of miR-128 was examined in invasive ductal breast cancer, and its relationship with clinicopathological features analysed. A series of in vitro and in vivo experiments were performed to investigate the function and mechanism of miR-128 in the development of invasive ductal breast cancer.

RESULTS

A cohort of 110 women with TNBC and 117 with non-TNBC were included in the study. In multivariable Cox regression analysis, overall and disease-free survival were significantly associated with lymph node metastasis, histological grade and molecular subtype. Subgroup analysis showed that low expression of miR-128 correlated with shorter overall and disease-free survival in TNBC (P < 0·001), and shorter overall but not disease-free survival in non-TNBC. In addition, miR-128 was able to inhibit glucose metabolism, mitochondrial respiration and proliferation of TNBC cells. These effects were consistent with miR-128 targeting inhibition of the insulin receptor and insulin receptor substrate 1.

CONCLUSION

MiR-128 might be a prognostic marker and possible molecular target for therapy in patients with TNBC.

Construction of an easy-to-use CRISPR-Cas9 system by patching a newly designed EXIT circuit

Background

Plasmid-borne genetic editing tools, including the widely used CRISPR-Cas9 system, have greatly facilitated bacterial programming to obtain novel functionalities. However, the lack of effective post-editing plasmid elimination methods impedes follow-up genetic manipulation or application. Conventional strategies including exposure to physical and chemical treatments, or exploiting temperature-sensitive replication origins have several drawbacks (e.g., they are limited for efficiency and are time-consuming). Therefore, the demand is apparent for easy and rapid elimination of the tool plasmids from their bacterial hosts after genetic manipulation.

Results

To bridge this gap, we designed a novel EXIT circuit with the homing endonuclease, which can be exploited for rapid and efficient elimination of various plasmids with diverse replication origins. As a proof of concept, we validated the EXIT circuit in Escherichia coli by harnessing homing endonuclease I-SceI and its cleavage site. When integrated into multiple plasmids with different origins, the EXIT circuit allowed them to be eliminated from the host cells, simultaneously. By combining the widely used plasmid-borne CRISPR-Cas9 system and the EXIT circuit, we constructed an easy-to-use CRISPR-Cas9 system that eliminated the Cas9- and the single-guide RNA (sgRNA)-encoding plasmids in one-step. Within 3 days, we successfully constructed an atrazine-degrading E. coli strain, thus further demonstrating the advantage of this new CRISPR-Cas9 system for bacterial genome editing.

Conclusions

Our novel EXIT circuit, which exploits the homing endonuclease I-SceI, enables plasmid(s) with different replication origins to be eliminated from their host cells rapidly and efficiently. We also developed an easy-to-use CRISPR-Cas9 system with the EXIT circuit, and this new system can be widely applied to bacterial genome editing.

Electronic supplementary material

The online version of this article (doi:10.1186/s13036-017-0072-5) contains supplementary material, which is available to authorized users.

Rational Design of an Ultrasensitive Quorum-Sensing Switch

One of the purposes of synthetic biology is to develop rational methods that accelerate the design of genetic circuits, saving time and effort spent on experiments and providing reliably predictable circuit performance. We applied a reverse engineering approach to design an ultrasensitive transcriptional quorum-sensing switch. We want to explore how systems biology can guide synthetic biology in the choice of specific DNA sequences and their regulatory relations to achieve a targeted function. The workflow comprises network enumeration that achieves the target function robustly, experimental restriction of the obtained candidate networks, global parameter optimization via mathematical analysis, selection and engineering of parts based on these calculations, and finally, circuit construction based on the principles of standardization and modularization. The performance of realized quorum-sensing switches was in good qualitative agreement with the computational predictions. This study provides practical principles for the rational design of genetic circuits with targeted functions.

[Advances in synthetic physiology of artificial genetic parts]

Artificial genetic parts should be modularized and can be predictably scaled up via assembly or reused in other contexts. Under intracellular physiological conditions, however, the functions of the assembled parts are severely impeded by multi-level physiological interference, i.e., most artificial assembled systems cannot be functional as predicted. Here we proposed a concept of synthetic physiology, defining it as the branch of synthetic biology to investigate and control interferences between artificial genetic parts and intracellular physiological system. Under such framework, we describe the part-host interactions and review the methods and strategies used to characterize and address these interactions.

Paired Design of dCas9 as a Systematic Platform for the Detection of Featured Nucleic Acid Sequences in Pathogenic Strains

We developed an in vitro DNA detection system using a pair of dCas9 proteins linked to split halves of luciferase. Luminescence was induced upon colocalization of the reporter pair to a ∼44 bp target sequence defined by sgRNAs. We used the system to detect Mycobacterium tuberculosis DNA with high specificity and sensitivity. The reprogrammability of dCas9 was further leveraged in an array design that accesses sequence information across the entire genome.

Semirational Approach for Ultrahigh Poly(3-hydroxybutyrate) Accumulation in Escherichia coli by Combining One-Step Library Construction and High-Throughput Screening

As a product of a multistep enzymatic reaction, accumulation of poly(3-hydroxybutyrate) (PHB) in Escherichia coli (E. coli) can be achieved by overexpression of the PHB synthesis pathway from a native producer involving three genes phbC, phbA, and phbB. Pathway optimization by adjusting expression levels of the three genes can influence properties of the final product. Here, we reported a semirational approach for highly efficient PHB pathway optimization in E. coli based on a phbCAB operon cloned from the native producer Ralstonia entropha (R. entropha). Rationally designed ribosomal binding site (RBS) libraries with defined strengths for each of the three genes were constructed based on high or low copy number plasmids in a one-pot reaction by an oligo-linker mediated assembly (OLMA) method. Strains with desired properties were evaluated and selected by three different methodologies, including visual selection, high-throughput screening, and detailed in-depth analysis. Applying this approach, strains accumulating 0%-92% PHB contents in cell dry weight (CDW) were achieved. PHB with various weight-average molecular weights (M_w) of 2.7-6.8 × 10⁶ were also efficiently produced in relatively high contents. These results suggest that the semirational approach combining library design, construction, and proper screening is an efficient way to optimize PHB and other multienzyme pathways.

Clinical efficacy of one stage posterior debridement joint graft fixation for lumbar vertebral fractures in spinal tuberculosis patients with compression

OBJECTIVE

Spinal tuberculosis, though destructive, can be cured in many patients by chemotherapy, though surgery is often necessary for decompression and deformity correction. Our aim of this study was to investigate the clinical efficacy of posterior debridement joint graft fixation therapy for lumbar vertebral fractures in patients with spinal tuberculosis with a compression fracture.

PATIENTS AND METHODS

We prospectively included 48 patients diagnosed with spinal tuberculosis and lumbar compression fracture in our hospital from June 2010 to June 2013. The patients were randomly divided into observation group (n = 27) and control group (n = 21). The patients in the control group underwent an anterior debridement joint bone fixation therapy, whereas, the patients in the observation group underwent one stage posterior debridement joint bone fixation therapy. The patients in the both groups were followed-up for about 2 years and the postoperative complications were recorded and analyzed.

RESULTS

Incision length, operative time and blood loss in patients of the observation group were significantly lower than the control group (p < 0.05). The kyphosis Cobb's angle was found to be reduced in a time-dependent manner in both groups, however, patients in the observation group achieved a significant reduction than the control (p < 0.05). The ASIA grade of few patients in the observation group significantly (p < 0.05) improved to class E from D at the time of the end of follow-up. The patients under the class 'excellent' and 'good' of Kirkaldy-Willis criteria were significantly (p < 05) higher in the observation group (92.6%) than the control group (85.7%). Also, the patients in the Bridwell grade I and II in the observation group (88.9%) were significantly (p < 0.05) higher in comparison with control group (81%). The prevalence of postoperative complications was significantly lower in the observation group (18.5%) when compared with the control group (28.6%).

CONCLUSIONS

Our results indicate that one-stage posterior debridement joint bone fixation therapy is an effective and safe procedure for patients with spinal tuberculosis and lumbar compression; this method is worthy of clinical application.

MiR-485-3p and miR-485-5p suppress breast cancer cell metastasis by inhibiting PGC-1α expression

Breast cancer is the worldwide leading cause of cancer mortality in women. The majority of deaths from breast cancer arise from metastasis of local tumors. Cancer cells support their rapid proliferation by diverting metabolites into anabolic pathways, but during cancer metastasis, the proliferative program of invasive cancer cells is suspended for a migratory phenotype. In this study, we demonstrated that both mature forms of miRNA-485, miR-485-3p and miR-485-5p were involved in regulating mitochondrial respiration, cell migration and cell invasion in breast cancer cells by directly targeting and inhibiting the expression of PGC-1α. Specifically, the expression levels of both miR-485-3p and miR-485-5p were decreased in breast cancer tissues. Overexpression of miR-485-3p and miR-485-5p suppressed mitochondrial respiration and potential for cell migration and invasion in vitro, and also inhibited spontaneous metastasis of breast cancer cells in vivo. The suppression of mitochondrial respiration and cell invasion could be partially relieved by restoration of PGC-1α expression.

Measurements of Gene Expression at Steady State Improve the Predictability of Part Assembly

Mathematical modeling of genetic circuits generally assumes that gene expression is at steady state when measurements are performed. However, conventional methods of measurement do not necessarily guarantee that this assumption is satisfied. In this study, we reveal a bi-plateau mode of gene expression at the single-cell level in bacterial batch cultures. The first plateau is dynamically active, where gene expression is at steady state; the second plateau, however, is dynamically inactive. We further demonstrate that the predictability of assembled genetic circuits in the first plateau (steady state) is much higher than that in the second plateau where conventional measurements are often performed. By taking the nature of steady state into consideration, our method of measurement promises to directly capture the intrinsic property of biological parts/circuits regardless of circuit-host or circuit-environment interactions.

Engineering Translational Activators with CRISPR-Cas System

RNA parts often serve as critical components in genetic engineering. Here we report a design of translational activators which is composed of an RNA endoribonuclease (Csy4) and two exchangeable RNA modules. Csy4, a member of Cas endoribonuclease, cleaves at a specific recognition site; this cleavage releases a cis-repressive RNA module (crRNA) from the masked ribosome binding site (RBS), which subsequently allows the downstream translation initiation. Unlike small RNA as a translational activator, the endoribonuclease-based activator is able to efficiently unfold the perfect RBS-crRNA pairing. As an exchangeable module, the crRNA-RBS duplex was forwardly and reversely engineered to modulate the dynamic range of translational activity. We further showed that Csy4 and its recognition site, together as a module, can also be replaced by orthogonal endoribonuclease-recognition site homologues. These modularly structured, high-performance translational activators would endow the programming of gene expression in the translation level with higher feasibility.

A novel approach for metabolic pathway optimization: Oligo-linker mediated assembly (OLMA) method

Background

Imbalances in gene expression of a metabolic pathway can result in less-yield of the desired products. Several targets were intensively investigated to balance the gene expression, such as promoter, ribosome binding site (RBS), the order of genes, as well as the species of the enzymes. However, the capability of simultaneous manipulation of multiple targets still needs to be explored.

Results

We reported a new DNA assembling method to vary all the above types of regulatory targets simultaneously, named oligo-linker mediated assembly (OLMA) method, which can incorporate up to 8 targets in a single assembly step. Two experimental cases were used to demonstrate the capability of the method: (1) assembly of multiple pieces of lacZ expression cassette; (2) optimization of four enzymes in lycopene biosynthetic pathway. Our results indicated that the OLMA method not only exploited larger combinatorial space, but also reduced the inefficient mutants.

Conclusions

The unique feature of oligo-linker mediated assembly (OLMA) method is inclusion of a set of chemically synthetic double-stranded DNA oligo library, which can be designed as promoters and RBSs, or designed with different overhang to bridge the genes in different orders. The inclusion of the oligos resulted in a PCR-free and zipcode-free DNA assembly reaction for OLMA.

Electronic supplementary material

The online version of this article (doi:10.1186/s13036-015-0021-0) contains supplementary material, which is available to authorized users.

Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters

The cloning of long DNA segments, especially those containing large gene clusters, is of particular importance to synthetic and chemical biology efforts for engineering organisms. While cloning has been a defining tool in molecular biology, the cloning of long genome segments has been challenging. Here we describe a technique that allows the targeted cloning of near-arbitrary, long bacterial genomic sequences of up to 100 kb to be accomplished in a single step. The target genome segment is excised from bacterial chromosomes in vitro by the RNA-guided Cas9 nuclease at two designated loci, and ligated to the cloning vector by Gibson assembly. This technique can be an effective molecular tool for the targeted cloning of large gene clusters that are often expensive to synthesize by gene synthesis or difficult to obtain directly by traditional PCR and restriction-enzyme-based methods.

Genomic engineering often requires the cloning of long DNA segments that contain large gene clusters. Here, the authors describe an RNA-guided Cas9 nuclease assisted in vitro technique that allows the targeted cloning of near-arbitrary, long bacterial genomic sequences of up to 100 kb in a single step.

Genetic programs constructed from layered logic gates in single cells

Genetic programs function to integrate environmental sensors, implement signal processing algorithms and control expression dynamics. These programs consist of integrated genetic circuits that individually implement operations ranging from digital logic to dynamic circuits, and they have been used in various cellular engineering applications, including the implementation of process control in metabolic networks and the coordination of spatial differentiation in artificial tissues. A key limitation is that the circuits are based on biochemical interactions occurring in the confined volume of the cell, so the size of programs has been limited to a few circuits. Here we apply part mining and directed evolution to build a set of transcriptional AND gates in Escherichia coli. Each AND gate integrates two promoter inputs and controls one promoter output. This allows the gates to be layered by having the output promoter of an upstream circuit serve as the input promoter for a downstream circuit. Each gate consists of a transcription factor that requires a second chaperone protein to activate the output promoter. Multiple activator-chaperone pairs are identified from type III secretion pathways in different strains of bacteria. Directed evolution is applied to increase the dynamic range and orthogonality of the circuits. These gates are connected in different permutations to form programs, the largest of which is a 4-input AND gate that consists of 3 circuits that integrate 4 inducible systems, thus requiring 11 regulatory proteins. Measuring the performance of individual gates is sufficient to capture the behaviour of the complete program. Errors in the output due to delays (faults), a common problem for layered circuits, are not observed. This work demonstrates the successful layering of orthogonal logic gates, a design strategy that could enable the construction of large, integrated circuits in single cells.

Combining transfer of TTF-1 and Pax-8 gene: a potential strategy to promote radioiodine therapy of thyroid carcinoma

Cotransfer of thyroid-specific transcription factor (TTF)-1 and Pax-8 gene to tumor cells, resulting in the re-expression of iodide metabolism-associated proteins, such as sodium iodide symporter (NIS), thyroglobulin (Tg), thyroperoxidase (TPO), offers the possibility of radioiodine therapy to non-iodide-concentrating tumor because the expression of iodide metabolism-associated proteins in thyroid are mediated by the thyroid transcription factor TTF-1 and Pax-8. The human TTF-1 and Pax-8 gene were transducted into the human thyroid carcinoma (K1 and F133) cells by the recombinant adenovirus, AdTTF-1 and AdPax-8. Re-expression of NIS mRNA and protein, but not TPO and Tg mRNA and protein, was detected in AdTTF-1-infected F133 cells, following with increasing radioiodine uptake (6.1-7.4 times), scarcely iodide organification and rapid iodide efflux (t(1/2) ≈ 8-min in vitro, t(1/2) ≈ 4.7-h in vivo). On contrast, all of the re-expression of NIS, TPO and Tg mRNA and proteins were detected in F133 cells coinfected with AdTTF-1 and AdPax-8. AdTTF-1- and AdPax-8-coinfected K1 and F133 cells could effectively accumulate radioiodine (6.6-7.5 times) and obviously retarded radioiodine retention (t(1/2) ≈ 25-30-min in vitro, t(1/2) ≈ 12-h in vivo) (P<0.05). Accordingly, the effect of radioiodine therapy of TTF-1 and Pax-8 cotransducted K1 and F133 cells (21-25% survival rate in vitro) was better than that of TTF-1-transducted cells (40% survival rate in vitro) (P<0.05). These results indicate that single TTF-1 gene transfer may have limited efficacy of radioiodine therapy because of rapid radioiodine efflux. The cotransduction of TTF-1 and Pax-8 gene, with resulting NIS-mediated radioiodine accumulation and TPO and Tg-mediated radioiodine organification and intracellular retention, may lead to effective radioiodine therapy of thyroid carcinoma.

A quantitative study of lambda-phage SWITCH and its components

We propose what we believe is a new model to quantitatively describe the lambda-phage SWITCH system. The model incorporates facilitated transfer mechanism of transcription factor, which can be simplified into a two-step reaction. We first sequentially obtain two indispensable parameters by fitting our model to experimental data of two simple systems, and then apply them to study the natural lambda-SWITCH system. By incorporating the facilitated transfer mechanism, we find that in RecA(-) host Escherichia coli, the wild-type lambda-lysogenic state is in a monostable regime rather than in a bistable regime. Furthermore, the model explains the weak role of Cro protein and probably sheds light on the evolution of lambda-Cro protein, which is known to be structurally distinct from the other Cros in lambdoid family members.

[Internal strontium-89 radiotherapy for malignant bony metastasis]

OBJECTIVE

This work was done to evaluate the indication, effectiveness, and side effects of internal radiotherapy with radioactive nuclide strontium-89 (89Sr) in patients with malignant metastasis in the bone.

METHODS

Fifty-six patients with skeletal metastasis received this internal radiotherapy. The patients were observed and followed up with respect to pain control, lesion improvement and side effects.

RESULTS

The overall effective rate of pain control was 76.8% with the effective rate of prostatic cancer and breast cancer higher than 80%. The lesions in 81.8% patients as assessed by SPECT imaging, were improved. The mild lowering of white cells, platelets and red cells was the main side effect.

CONCLUSION

Internal radiotherapy with 89Sr is very useful for patients with malignant cancer metastasis in the bone.

Sexual behaviour and contraceptive use among unmarried, young women migrant workers in five cities in China

This paper reports the results of exploratory research on reproductive and sexual health knowledge and sexual behaviour of young, unmarried women who migrate to cities from rural areas for work, and their access to and needs in relation to family planning in Beijing, Guangzhou, Shanghai, Guiyang and Taiyuan, in China. Focus group discussions were conducted with 146 young women aged 16-25 and 58 in-depth interviews with key informants. Some of the young female migrant workers were sexually active and living with their boyfriends, most of whom expected to marry each other. Most of the women lacked basic information about reproduction and contraception, and did not know where or how to obtain contraception. There were social, psychological and economic barriers to accessing services. Only a small proportion of those who were unmarried were using contraception, so induced abortion was often the outcome of unprotected premarital sex. Pleasing male partners also played an important role in unprotected sex. The training, attitudes and approach of the entire family planning service system in relation to unmarried and young people in China, including this migrant population, needs to be reorientated so as to provide them with appropriate and adequate services.

The mechanism of the effect of obesity in knee osteoarthritis: the mediating role of malalignment

OBJECTIVE

Obesity is most strongly linked to osteoarthritis (OA) at the knee. Varus malalignment was examined as a possible local mediator that may increase the impact of body weight at the knee, versus the hip or ankle. Compartment load distribution is more equitable in valgus than in varus knees, and valgus knees may better tolerate obesity. We therefore tested whether 1) body mass index (BMI) is correlated with OA severity in varus knees, 2) the BMI-OA severity correlation is weaker in valgus than in varus knees, 3) BMI is correlated with the severity of varus malalignment, and 4) the BMI-medial tibiofemoral OA severity relationship is reduced after controlling for varus malalignment.

METHODS

In 300 community-recruited patients with knee OA, 2 groups (varus and valgus) were identified based on dominant knee alignment on a full-limb radiograph, i.e., the angle formed by the intersection of the femoral and tibial mechanical axes. Severity of knee OA was assessed by measurement of the narrowest joint space width on radiographs of knees in a fluoroscopy-confirmed semiflexed position.

RESULTS

Alignment direction was symmetric (or neutral in 1 limb) in 87% of patients. One hundred fifty-four patients had varus knees and 115 had valgus knees. BMI correlated with OA severity in the varus group (r = -0.29, P = 0.0009) but not in the valgus group (r = -0.13, P = 0.17). BMI correlated with malalignment in those with varus knees (r = 0.26) but not in those with valgus knees (r = 0.16). The partial correlation of BMI and OA severity, controlling for sex, was reduced from 0.24 (P = 0.002) to 0.04 (P = 0.42) when varus malalignment was added to the model.

CONCLUSION

BMI was related to OA severity in those with varus knees but not in those with valgus knees. Much of the effect of BMI on the severity of medial tibiofemoral OA was explained by varus malalignment, after controlling for sex. Whether it precedes or follows the onset of disease, varus malalignment is one local factor that may contribute to rendering the knee most vulnerable to the effects of obesity.

The effect of gestational parity on FEV1 in a group of healthy volunteer women

In the past, studies utilizing within-subject comparisons of small groups of pregnant women showed that forced expiratory volume in 1 s (FEV1) remained essentially unchanged during pregnancy. However, one of the findings from an epidemiological study was that women with greater number of children experienced a faster decline of FEV1. The aim of this study was to examine the effect of parity on FEV1 in a group of healthy volunteer women. To this end, cross-sectional multiple regression analyses of data from 397 healthy women participants in the Baltimore Longitudinal Study of Aging (BLSA) with a mean (range) age of 47.7 (18-92) years were performed. Similar analyses were done using the younger (50 years or less) and the older (> 50 years) subgroups. After controlling for age, height, weight, and smoking, parity as a dichotomous variable was associated with a higher FEV1 in women of child-bearing age (0.139 1; P = 0.02) but not in the older women. There was a modest link with the number of children (P = 0.05), with the first child possibly having the greatest effect on FEV1. We could not account for the effect of parity on FEV1 by the educational level, occupation, health status of the women, or by the presence of a cohort effect. Thus the nulliparous state is associated with lower FEV1 in this group of healthy adult women of child-bearing age.

Laxity in healthy and osteoarthritic knees

OBJECTIVE

Although it is a cause of osteoarthritis (OA) in animal models, laxity in human knee OA has been minimally evaluated. Ligaments become more compliant with age; whether this results in clinical laxity is not clear. In theory, laxity may predispose to OA and/or result from OA. Our goals were to examine the correlation of age and sex with knee laxity in control subjects without OA, compare laxity in uninvolved knees of OA patients with that in older control knees, and examine the relationship between specific features of OA and knee laxity.

METHODS

We assessed varus-valgus and anteroposterior laxity in 25 young control subjects, 24 older control subjects without clinical OA, radiographic OA, or a history of knee injury, and 164 patients with knee OA as determined by the presence of definite osteophytes. A device was designed to assess varus-valgus laxity under a constant varus or valgus load while maintaining a fixed knee flexion angle and thigh and ankle immobilization. Radiographic evaluations utilized protocols addressing position, beam alignment, magnification, and landmark definition; the semiflexed position was used, with fluoroscopic confirmation.

RESULTS

In the controls, women had greater varus-valgus laxity than did men (3.6 degrees versus 2.7 degrees; 95% confidence interval [95% CI] of difference 0.38, 1.56; P = 0.004), and laxity correlated modestly with age (r = 0.29, P = 0.04). Varus-valgus laxity was greater in the uninvolved knees of OA patients than in older control knees (4.9 degrees versus 3.4 degrees; 95% CI of difference 0.60, 2.24; P = 0.0006). In OA patients, varus-valgus laxity increased as joint space decreased (slope -0.34; 95% CI -0.48, -0.19; P < 0.0001) and was greater in knees with than in knees without bony attrition (5.3 degrees versus 4.5 degrees; 95% CI of difference 0.32, 1.27; P = 0.001).

CONCLUSION

Greater varus-valgus laxity in the uninvolved knees of OA patients versus older control knees and an age-related increase in varus-valgus laxity support the concept that some portion of the increased laxity of OA may predate disease. Loss of cartilage/bone height is associated with greater varus-valgus laxity. These results raise the possibility that varus-valgus laxity may increase the risk of knee OA and cyclically contribute to progression.

Does laxity alter the relationship between strength and physical function in knee osteoarthritis?

OBJECTIVE

Since strengthening interventions have had a lower-than-expected impact on patient function in studies of knee osteoarthritis (OA) and it is known that laxity influences muscle activity, this study examined whether the relationship between strength and function is weaker in the presence of laxity.

METHODS

One hundred sixty-four patients with knee OA were studied. Knee OA was defined by the presence of definite osteophytes, and patients had to have at least a little difficulty with knee-requiring activities. Tests were performed to determine quadriceps and hamstring strength, varus-valgus laxity, functional status (Western Ontario and McMaster Universities Osteoarthritis Index Physical Functioning subscale [WOMAC-PF] and chair-stand performance), body mass index, and pain. High and low laxity groups were defined as above and below the sample median, respectively.

RESULTS

Strength and chair-stand rates correlated (r = 0.44 to 0.52), as did strength and the WOMAC-PF score (r = -0.21 to -0.36). In multivariate analyses, greater laxity was consistently associated with a weaker relationship between strength (quadriceps or hamstring) and physical functioning (chair-stand rate or WOMAC-PF score).

CONCLUSION

Varus-valgus laxity is associated with a decrease in the magnitude of the relationship between strength and physical function in knee OA. In studies examining the functional and structural consequences of resistance exercise in knee OA, stratification of analyses by varus-valgus laxity should be considered. The effect of strengthening interventions in knee OA may be enhanced by consideration of the status of the passive restraint system.