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PubMed2026

Modular synthetic cross-kingdom promoters enable coordinated expression in Escherichia coli and Saccharomyces cerevisiae.

Synthetic biology and metabolic engineering increasingly demand predictable and interoperable gene expression across phylogenetically distant organisms, as the need for portable genetic systems and transferable metabolic pathways continues to grow. However, fundamental differences in promoter architecture and transcriptional logic across kingdoms remain a key bottleneck in developing universal expression platforms. Here, we designed a set of modular hybrid promoters that enable tunable and quantitatively consistent gene expression in both Escherichia coli and Saccharomyces cerevisiae. These promoters integrate bacterial -10/-35 motifs and Shine-Dalgarno sequences with minimal yeast TATA boxes and Kozak sequences to ensure transcriptional and translational compatibility. The promoter set supported weak, moderate, and strong expression with high relative consistency across species. Applied to the biosynthetic pathway for the valuable pigment prodeoxyviolacein, the hybrid promoters enabled coordinated production in both hosts. This work establishes a broadly compatible promoter architecture and provides a foundational toolkit for cross-kingdom, multi-host synthetic biology.

Promoter Regions, Genetic↗
PubMed2003

ExpressYourself: A modular platform for processing and visualizing microarray data.

DNA microarrays are widely used in biological research; by analyzing differential hybridization on a single microarray slide, one can detect changes in mRNA expression levels, increases in DNA copy numbers and the location of transcription factor binding sites on a genomic scale. Having performed the experiments, the major challenge is to process large, noisy datasets in order to identify the specific array elements that are significantly differentially hybridized. This normally requires aggregating different, often incompatible programs into a multi-step pipeline. Here we present ExpressYourself, a fully integrated platform for processing microarray data. In completely automated fashion, it will correct the background array signal, normalize the Cy5 and Cy3 signals, score levels of differential hybridization, combine the results of replicate experiments, filter problematic regions of the array and assess the quality of individual and replicate experiments. ExpressYourself is designed with a highly modular architecture so various types of microarray analysis algorithms can readily be incorporated as they are developed; for example, the system currently implements several normalization methods, including those that simultaneously consider signal intensity and slide location. The processed data are presented using a web-based graphical interface to facilitate comparison with the original images of the array slides. In particular, Express Yourself is able to regenerate images of the original microarray after applying various steps of processing, which greatly facilities identification of position-specific artifacts. The program is freely available for use at http://bioinfo.mbb.yale.edu/expressyourself.

Algorithms↗
PubMed2004

Mer1p is a modular splicing factor whose function depends on the conserved U2 snRNP protein Snu17p.

Mer1p activates the splicing of at least three pre-mRNAs (AMA1, MER2, MER3) during meiosis in the yeast Saccharomyces cerevisiae. We demonstrate that enhancer recognition by Mer1p is separable from Mer1p splicing activation. The C-terminal KH-type RNA-binding domain of Mer1p recognizes introns that contain the Mer1p splicing enhancer, while the N-terminal domain interacts with the spliceosome and activates splicing. Prior studies have implicated the U1 snRNP and recognition of the 5' splice site as key elements in Mer1p-activated splicing. We provide new evidence that Mer1p may also function at later steps of spliceosome assembly. First, Mer1p can activate splicing of introns that have mutated branch point sequences. Secondly, Mer1p fails to activate splicing in the absence of the non-essential U2 snRNP protein Snu17p. Thirdly, Mer1p interacts with the branch point binding proteins Mud2p and Bbp1p and the U2 snRNP protein Prp11p by two-hybrid assays. We conclude that Mer1p is a modular splicing regulator that can activate splicing at several early steps of spliceosome assembly and depends on the activities of both U1 and U2 snRNP proteins to activate splicing.

Base Sequence↗
PubMed2006

A modular DNA signal translator for the controlled release of a protein by an aptamer.

Owing to the intimate linkage of sequence and structure in nucleic acids, DNA is an extremely attractive molecule for the development of molecular devices, in particular when a combination of information processing and chemomechanical tasks is desired. Many of the previously demonstrated devices are driven by hybridization between DNA 'effector' strands and specific recognition sequences on the device. For applications it is of great interest to link several of such molecular devices together within artificial reaction cascades. Often it will not be possible to choose DNA sequences freely, e.g. when functional nucleic acids such as aptamers are used. In such cases translation of an arbitrary 'input' sequence into a desired effector sequence may be required. Here we demonstrate a molecular 'translator' for information encoded in DNA and show how it can be used to control the release of a protein by an aptamer using an arbitrarily chosen DNA input strand. The function of the translator is based on branch migration and the action of the endonuclease FokI. The modular design of the translator facilitates the adaptation of the device to various input or output sequences.

Aptamers, Nucleotide↗
PubMed2002

Advanced modular self-inactivating lentiviral expression vectors for multigene interventions in mammalian cells and in vivo transduction.

In recent years, lentiviral expression systems have gained an unmatched reputation among the gene therapy community for their ability to deliver therapeutic transgenes into a wide variety of difficult-to-transfect/transduce target tissues (brain, hematopoietic system, liver, lung, retina) without eliciting significant humoral immune responses. We have cloned a construction kit-like self-inactivating lentiviral expression vector family which is compatible to state-of-the-art packaging and pseudotyping technologies and contains, besides essential cis-acting lentiviral sequences, (i) unparalleled polylinkers with up to 29 unique sites for restriction endonucleases, many of which recognize 8 bp motifs, (ii) strong promoters derived from the human cytomegalovirus immediate-early promoter (P(hCMV)) or the human elongation factor 1alpha (P(hEF1)(alpha)), (iii) P(hCMV-) or P(PGK-) (phosphoglycerate kinase promoter) driven G418 resistance markers or fluorescent protein-based expression tracers and (iv) tricistronic expression cassettes for coordinated expression of up to three transgenes. In addition, we have designed a size-optimized series of highly modular lentiviral expression vectors (pLenti Module) which contain, besides the extensive central polylinker, unique restriction sites flanking any of the 5'U3, R-U5-psi+-SD, cPPT-RRE-SA and 3'LTR(DeltaU3) modules or placed within the 5'U3 (-78 bp) and 3'LTR(DeltaU3) (8666 bp). pLentiModule enables straightforward cassette-type module swapping between lentiviral expression vector family members and facilitates the design of Tat-independent (replacement of 5'LTR by heterologous promoter elements), regulated and self-excisable proviruses (insertion of responsive operators or LoxP in the 3'LTR(DeltaU3) element). We have validated our lentiviral expression vectors by transduction of a variety of insect, chicken, murine and human cell lines as well as adult rat cardiomyocytes, rat hippocampal slices and chicken embryos. The novel multi-purpose construction kit-like vector series described here is compatible with itself as well as many other (non-viral) mammalian expression vectors for straightforward exchange of key components (e.g. promoters, LTRs, resistance genes) and will assist the gene therapy and tissue engineering communities in developing lentiviral expression vectors tailored for optimal treatment of prominent human diseases.

Animals↗
PubMed1998

Prediction of protein hydration sites from sequence by modular neural networks.

The hydration properties of a protein are important determinants of its structure and function. Here, modular neural networks are employed to predict ordered hydration sites using protein sequence information. First, secondary structure and solvent accessibility are predicted from sequence with two separate neural networks. These predictions are used as input together with protein sequences for networks predicting hydration of residues, backbone atoms and sidechains. These networks are trained with protein crystal structures. The prediction of hydration is improved by adding information on secondary structure and solvent accessibility and, using actual values of these properties, residue hydration can be predicted to 77% accuracy with a Matthews coefficient of 0.43. However, predicted property data with an accuracy of 60-70% result in less than half the improvement in predictive performance observed using the actual values. The inclusion of property information allows a smaller sequence window to be used in the networks to predict hydration. It has a greater impact on the accuracy of hydration site prediction for backbone atoms than for sidechains and for non-polar than polar residues. The networks provide insight into the mutual interdependencies between the location of ordered water sites and the structural and chemical characteristics of the protein residues.

Amino Acid Sequence↗
PubMed1987

Modular transport ventilation system for twins.

A single modular transport ventilation system has been modified for ventilation of twins by duplicating the gas supply lines, gas blender, and ventilator. This twin ventilator system can be assembled easily in minutes, has essential built-in safety features, and provides simultaneous yet individualized ventilation support to each infant during transport without the need for additional personnel.

Equipment Design↗
PubMed1999

Modular glovebox connector and associated good practices for control of radioactive and chemically toxic materials.

Design and associated good practices are described for a modular glovebox connector to improve control of radioactive and chemically toxic materials. The connector consists of an anodized aluminum circular port with a mating spacer, gaskets, and retaining rings for joining two parallel ends of commercially available or custom-manufactured glovebox enclosures. Use of the connector allows multiple gloveboxes to be quickly assembled or reconfigured in functional units. Connector dimensions can be scaled to meet operational requirements for access between gloveboxes. Options for construction materials are discussed, along with recommendations for installation of the connector in new or retrofitted systems. Associated good practices include application of surface coatings and caulking, use of disposable glovebags, and proper selection and protection of gasket and glove materials. Use of the connector at an inhalation toxicology research facility has reduced the time and expense required to reconfigure equipment for changing operational requirements, the dispersion of contamination during reconfigurations, and the need for decommissioning and disposal of contaminated enclosures.

Aluminum↗
PubMed2002

A competency-based modular learning program.

This article describes a take-home competency-based modular learning system that includes posttesting and a hands-on competency validation. This successful program assisted in improving nursing skills, nurse satisfaction, and quality of care. Although used with pediatric clinicians, this program can be adapted to any type agency or staff competencies.

Attitude of Health Personnel↗
PubMedDate not supplied

Hip arthrodesis using the AO modular external fixator.

Arthrodesis remains the treatment of choice for children and young adults with deteriorated, painful hip joints. In 1992, Fernandez Dell'Oca et al. reported on the use of the AO external fixator in hip arthrodesis. Three patients who underwent this procedure are reported. Hip arthrodesis with AO modular external fixator has all the benefits of the Thompson arthrodesis, with the added advantages of producing a solid fusion in the correct position and allowing the patient to remain ambulatory while using the external fixator.

Adolescent↗
PubMed2005

What's the difference? Contrasting modular and neural network approaches to understanding developmental variability.

Understanding why development differs across individuals is an important challenge for developmental theory. This paper evaluates two approaches to developmental variability observed in domains such as language processing and across populations such as typically developing children, children with developmental disorders, and typical adults. Modular accounts attribute developmental variability to delay, damage, or dysfunction in discrete underlying structures. Neural network approaches attribute developmental variability to emergent effects of graded variations in an interactive, developing system. The authors conclude that neural network approaches offer more formal and parsimonious accounts of the nature and sources of developmental variability.

Child↗
PubMed1998

Clinical results using the trochanter stabilizing plate (TSP): the modular extension of the dynamic hip screw (DHS) for internal fixation of selected unstable intertrochanteric fractures.

OBJECTIVE: To evaluate whether the implantation of the modular trochanter stabilizing plate (TSP) in addition to the dynamic hip screw (DHS) prevents excessive telescoping and limb shortening in four-part and selected three-part trochanteric fractures. DESIGN: Prospective clinical study. SETTING: The study was conducted at the trauma unit of the Surgical Department of the University of Basel, Switzerland. PATIENTS: Forty-six consecutive patients with unstable intertrochanteric fractures were treated with an additional TSP super-imposed on the regular DHS at our institution between July 1991 and July 1993. Five patients died before the first follow-up, one patient was lost to follow-up, and another patient refused follow-up. Thus, thirty-nine patients were followed for at least twelve months (mean 14 months, range 12 to 20 months). INTERVENTION: The fractures treated were classified according to the OTA classification, which is based on the AO classification. Seventeen were 31-A2.2, seven were 31-A2.3, and fourteen were 31-A3.3 fractures. RESULTS: Lateralization of the greater trochanter was successfully prevented in all fractures. Limited fracture impaction was found in 90 percent (n = 35) of the patients with telescoping of 9.5 millimeters (range 0 to 30 millimeters), resulting in mean limb shortening of 5.37 millimeters (range 0 to 14.9 millimeters). Four patients suffered limb shortening exceeding fifteen millimeters (range 15.6 to 21.3 millimeters). Functional results were excellent and good in 87 percent of patients and fair in 13 percent according to the Salvati-Wilson score. All fractures had healed six months after the operation. Three complications required a secondary procedure: one from not inserting a second screw parallel to the gliding hip screw to prevent rotation of the head-neck fragment ("antirotation screw"), one because of deep infection, and one because of a refracture after premature implant removal. CONCLUSION: In unstable pertrochanteric fractures with small or missing lateral cortical buttress, the addition of a TSP to the DHS effectively supports the unstable greater trochanter fragment and can prevent rotation of the head-neck fragment. Excessive fracture impaction and consecutive limb shortening was prevented by this additional implant in 90 percent of these patients.

Adult↗
PubMed1980

Modular approach to CPR training.

Basic and advanced cardiopulmonary resuscitation training is worthwhile yet time consuming. Anesthesiologists should be among the most qualified leaders in CPR teaching programs. Using a modular self-teaching presentation for basic and advanced cardiac life support courses, minimal instructor time is required to accomplish proficiency in both didactic and mannequin performance for participants. This method can be adapted to various educational levels and time constraints without compromising quality of teaching.

Anesthesiology↗
PubMed2003

Polyethylene damage on the nonarticular surface of modular total knee prostheses.

Modular tibial implants submitted for retrieval analysis were examined for evidence of cold flow, wear, or polyethylene failure. All retrieved components showed areas of cold flow and wear. Significant damage, defined as pitting, gouging, or delamination was observed in 77% of the retrieved implants. Cold flow deformation commonly was observed at the junction of the polyethylene and locking mechanisms or junction of the polyethylene and the edge of the tibial tray. Control implants did not show such areas of damage. Clinical factors such as age, activity status, length of implantation, limb alignment before revision, and thickness of the tibial insert did not correlate with backside wear. No association was found between polyethylene thickness, time of implantation, limb or prosthesis alignment, or activity status or weight of the patient.

Adult↗
PubMed2004

Factors influencing wear and osteolysis in press-fit condylar modular total knee replacements.

The purpose of this study was to determine the factors influencing wear and osteolysis in patients who have had total knee arthroplasty with the Press-Fit Condylar modular system. Two-thousand ninety-one primary total knee replacements in 1737 patients were done using the Press-Fit Condylar system at three centers. Radiographic and manufacturing data were obtained for 2016 of the 2091 implants (96.4%). For the 1287 of 2016 knees (64%) with more than 5 years of followup, the prevalence of wear-related failure was 8.3%. The 13-year survivorship for all patients was 82.6%. Cox hazards analysis revealed five variables that were correlated with wear-related failure: patient age, patient gender, polyethylene sheet vendor, polyethylene finishing method, and polyethylene shelf age. We were unable to identify one factor as the defining reason for these wear-related failures. The multiple changes in manufacturing methods during the life of this implant may have precluded such a determination. These results may be specific to inserts sterilized in air with gamma irradiation and should not be generalized to current manufacturing techniques. This study emphasizes the potential deleterious effects that small changes in the manufacturing process may have on the outcome of a prosthesis with an initially favorable survivorship.

Adult↗
PubMed2005

A modular prosthesis for patellofemoral arthroplasty: design and initial results.

UNLABELLED: This study was designed to determine if a new and modular prosthesis for patellofemoral arthroplasty would produce results at least as good as those reported for other designs, while simultaneously eliminating the risks of patellar revision should total knee arthroplasty be needed in the future. Another issue was its suitability for the older patient with isolated patellofemoral arthritis in order to avoid destruction of the normal femoro-tibial compartments involved in total knee arthroplasty. Finally, I sought information about the safety and longevity of this prosthesis when used for patellofemoral arthroplasty in severely disabled patients too young to be considered for total knee replacement. From a cohort of 16 patients (8 studied retrospectively and 8 prospectively), aged 26 to 81 years, and followed up for 2.75-6.25 years, 15 (94%) rated their results excellent or good using the Activities of Daily Living Scale. These results are better than previously reported for other prosthetic designs. To date, no patient in this study group has required conversion to a total knee arthroplasty. The design has proven safe for use in both the older and younger patient, but longer followup will be needed to assess greater longevity. LEVEL OF EVIDENCE: Therapeutic Study, Level IV-8 (case series--no, or historical control group). See the Guidelines for Authors for a complete description of levels of evidence.

Activities of Daily Living↗
PubMed2006

Modular femoral offset stems facilitate joint line restoration in revision knee arthroplasty.

UNLABELLED: Restoration of proper joint line position in revision total knee arthroplasty is essential in promoting recovery of function. We retrospectively analyzed joint line restoration and clinical outcomes in 22 consecutive femur revision cases using modular offsets of variable length and direction between the intramedullary fixation rod and the femoral component. Flexion and extension gap balancing techniques and medial epicondylar referencing was used to achieve proper position of the joint line. Position of the reconstructed joint line from postoperative radiographs was compared to the baseline position of intended anatomic placement determined from pre-operative planning radiographs. Postoperative joint line height averaged 1.6 mm distal to baseline (range, 5 mm distal to 2.5 proximal). Joint line was restored to within 2 mm of anatomic position in 12 of the 22 knees. Sixteen patients received conventional, minimally constrained tibial inserts, and joint stability was achieved in all cases. LEVEL OF EVIDENCE: Therapeutic study, Level IV (case series). See Guidelines for Authors for a complete description of levels of evidence.

Adult↗
PubMed2006

Comprehensive analysis of cantilever, translational, and modular corrective techniques in adults with scoliosis treated with surgery to the sacropelvis.

BACKGROUND: The treatment of adults with scoliosis has been the source of debate over the last several decades. Pain associated with curve progression and decompensation is the most common presenting scenario and surgical management is often indicated. Correction of these deformities may involve long segment fusions to the sacrum and pelvis. Most authors have reported high rates of complications associated with this procedure. There remains little consensus with regard to the treatment of this challenging condition. PURPOSE: The purpose of this study was to evaluate the clinical and radiographic outcomes of patients treated with long fusions to the sacrum and pelvis using third generation instrumentation techniques. These included the use of cantilever, translational, and modular corrective techniques. METHODS: Inpatient and outpatient charts were reviewed for 97 patients (89 women and 8 men). The average age was 55 years (27 to 78 y). The information obtained included patient age, sex, comorbidities, perioperative complications, and long-term clinical outcome. Standing radiographic coronal and sagittal measurements were recorded preoperatively, immediately postoperatively, and at the most recent follow-up visit. RESULTS: Eighty-nine patients underwent combined anterior and posterior surgery, whereas 8 patients were treated with posterior-only procedures. Two patients had fixation to the sacrum without extension into the ilium. Structural curves averaged 53 degrees preoperatively, 32 degrees postoperatively, and 33 degrees at follow-up. Thoracic kyphosis averaged +36 degrees preoperatively, +39 degrees postoperatively, and +46 degrees at follow-up. Lumbar lordosis averaged -41 degrees preoperatively, -48 degrees postoperatively, and -48 degrees at follow-up. Coronal imbalance averaged 2.9 cm preoperatively, 2.4 cm postoperatively, and 2.3 cm at follow-up. Sagittal imbalance averaged 6.8 cm preoperatively, 2.9 cm postoperatively, and 3.6 cm at follow-up. Major complications included pseudarthrosis (10%), deep infection (13%), painful iliac fixation (20%), neurologic injury (6%), need for some form of revision surgery (39%), chronic severe pain (2%), pulmonary embolism (2%), and deep venous thrombosis (2%). There were no permanent neurologic injuries or deaths related to the surgery.

Adult↗