A simple, robust, broadly applicable insertion mutagenesis method to create random fluorescent protein: target protein fusions.

A simple, broadly applicable method was developed using an in vitro transposition reaction followed by transformation into Escherichia coli and screening plates for fluorescent colonies. The transposition reaction catalyzes the random insertion of a fluorescent protein open reading frame into a target gene on a plasmid. The transposition reaction is employed directly in an E. coli transformation with no further procedures. Plating at high colony density yields fluorescent colonies. Plasmids purified from fluorescent colonies contain random, in-frame fusion proteins into the target gene. The plate screen also results in expressed, stable proteins. A large library of chimeric proteins was produced, which was useful for downstream research. The effect of using different fluorescent proteins was investigated as well as the dependence of the linker sequence between the target and fluorescent protein open reading frames. The utility and simplicity of the method were demonstrated by the fact that it has been employed in an undergraduate biology laboratory class without failure over dozens of class sections. This suggests that the method will be useful in high-impact research at small liberal arts colleges with limited resources. However, in-frame fusion proteins were obtained from 8 different targets suggesting that the method is broadly applicable in any research setting.

Natural immunity to malaria preferentially targets the endothelial protein C receptor-binding regions of PfEMP1s.

Antibody responses to variant surface antigens (VSAs) produced by the malaria parasite Plasmodium falciparum may contribute to age-related natural immunity to severe malaria. One VSA family, P. falciparum erythrocyte membrane protein-1 (PfEMP1), includes a subset of proteins that binds endothelial protein C receptor (EPCR) in human hosts and potentially disrupts the regulation of inflammatory responses, which may lead to the development of severe malaria. We probed peptide microarrays containing segments spanning five PfEMP1 EPCR-binding domain variants with sera from 10 Malian adults and 10 children to determine the differences between adult and pediatric immune responses. We defined serorecognized peptides and amino acid residues as those that elicited a significantly higher antibody response than malaria-naïve controls. We aimed to identify regions consistently serorecognized among adults but not among children across PfEMP1 variants, potentially indicating regions that drive the development of immunity to severe malaria. Adult sera consistently demonstrated broader and more intense serologic responses to constitutive PfEMP1 peptides than pediatric sera, including peptides in EPCR-binding domains. Both adults and children serorecognized a significantly higher proportion of EPCR-binding peptides than peptides that do not directly participate in receptor binding, indicating a preferential development of serologic responses at functional residues. Over the course of a single malaria transmission season, pediatric serological responses increased between the start and the peak of the season, but waned as the transmission season ended. IMPORTANCE Severe malaria and death related to malaria disproportionately affect sub-Saharan children under 5 years of age, commonly manifesting as cerebral malaria and/or severe malarial anemia. In contrast, adults in malaria-endemic regions tend to experience asymptomatic or mild disease. Our findings indicate that natural immunity to malaria targets specific regions within the EPCR-binding domain, particularly peptides containing EPCR-binding residues. Epitopes containing these residues may be promising targets for vaccines or therapeutics directed against severe malaria. Our approach provides insight into the development of natural immunity to a binding target linked to severe malaria by characterizing an "adult-like" response as recognizing a proportion of epitopes within the PfEMP1 protein, particularly regions that mediate EPCR binding. This "adult-like" response likely requires multiple years of malaria exposure, as increases in pediatric serologic response over a single malaria transmission season do not appear significant.

Impedimetric Polyaniline-Based Aptasensor for Aflatoxin B1 Determination in Agricultural Products.

An impedimetric aptasensor based on a polyaniline (PAni) support matrix is developed through the surface modification of a screen-printed carbon electrode (SPE) for aflatoxin B1 (AFB1) detection in foodstuffs and feedstuffs for food safety. The PAni is synthesized with the chemical oxidation method and characterized with potentiostat/galvanostat, FTIR, and UV-vis spectroscopy techniques. The stepwise fabrication procedure of the PAni-based aptasensor is characterized by means of cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS) methods. The impedimetric aptasensor is optimized using the EIS technique, and its feasibility of detecting AFB1 in real sample matrices is evaluated via a recovery study in spiked foodstuffs and feedstuffs, such as pistachio nuts, cinnamons, cloves, corn, and soybeans, with a good recovery percentage, ranging from 87.9% to 94.7%. The charge transfer resistance (RCT) at the aptasensor interface increases linearly with the AFB1 concentration in the range of 3 × 10-2 nM to 8 × 10-2 nM, with a regression coefficient (R2) value of 0.9991 and detection limit of 0.01 nM. The proposed aptasensor is highly selective towards AFB1 and partially selective to AFB2 and ochratoxin A (OTA) due to their similar structures that differ only at the carbon-carbon double bond located at C8 and C9 and the large molecule size of OTA.

Online Courses Provide Robust Learning Gains and Improve Learner Confidence in the Foundational Biomedical Sciences.

The early stages of medical school involve education in a number of foundational biomedical sciences including genetics, immunology, and physiology. However, students entering medical school may have widely varying levels of background in these areas due to differences in the availability and quality of prior education on these topics. Even students who have recently taken formal courses in these subjects may not feel confident in their level of preparation, leading to anxiety for early-stage medical students. These differences can make it difficult for instructors to create meaningful learning experiences that are appropriate for all students. Additionally, actual or perceived differences in preparation may lead fewer students from diverse backgrounds to apply to medical school. Therefore, creating an efficient and scalable way to increase students' knowledge and confidence in these topics addresses an important need for many medical schools. We recorded pre- and post-course quiz scores for 9790 individuals who completed HMX online courses, developed in accordance with evidence-based learning practices and covering the fundamentals of biochemistry, genetics, immunology, pharmacology, and physiology. Each question was accompanied by a Likert scale question to assess the learner's confidence in their answer. Learners' median post-course quiz performance and self-assessed confidence significantly increased relative to pre-course quiz performance for each course. Improvements were consistent across US-based medical schools, non-US medical schools, and course runs open to the public. This indicates that online courses created using evidence-based learning practices can lead to significant increases in knowledge and confidence for many learners, helping prepare them for further medical education. Supplementary Information: The online version contains supplementary material available at 10.1007/s40670-022-01660-4.

Unlocking the thermoelectric potential of the Ca14AlSb11 structure type.

Yb14MnSb11 and Yb14MgSb11 are among the best p-type high-temperature (>1200 K) thermoelectric materials, yet other compounds of this Ca14AlSb11 structure type have not matched their stability and efficiency. First-principles computations show that the features in the electronic structures that have been identified to lead to high thermoelectric performances are present in Yb14ZnSb11, which has been presumed to be a poor thermoelectric material. We show that the previously reported low power factor of Yb14ZnSb11 is not intrinsic and is due to the presence of a Yb9Zn4+xSb9 impurity uniquely present in the Zn system. Phase-pure Yb14ZnSb11 synthesized through a route avoiding the impurity formation reveals its exceptional high-temperature thermoelectric properties, reaching a peak zT of 1.2 at 1175 K. Beyond Yb14ZnSb11, the favorable band structure features for thermoelectric performance are universal among the Ca14AlSb11 structure type, opening the possibility for high-performance thermoelectric materials.

Temperature-Dependent Coherent Tunneling across Graphene-Ferritin Biomolecular Junctions.

Understanding the mechanisms of charge transport (CT) across biomolecules in solid-state devices is imperative to realize biomolecular electronic devices in a predictive manner. Although it is well-accepted that biomolecule-electrode interactions play an essential role, it is often overlooked. This paper reveals the prominent role of graphene interfaces with Fe-storing proteins in the net CT across their tunnel junctions. Here, ferritin (AfFtn-AA) is adsorbed on the graphene by noncovalent amine-graphene interactions confirmed with Raman spectroscopy. In contrast to junctions with metal electrodes, graphene has a vanishing density of states toward its intrinsic Fermi level ("Dirac point"), which increases away from the Fermi level. Therefore, the amount of charge carriers is highly sensitive to temperature and electrostatic charging (induced doping), as deduced from a detailed analysis of CT as a function of temperature and iron loading. Remarkably, the temperature dependence can be fully explained within the coherent tunneling regime due to excitation of hot carriers. Graphene is not only demonstrated as an alternative platform to study CT across biomolecular tunnel junctions, but it also opens rich possibilities in employing interface electrostatics in tuning CT behavior.

Increased posterior tibial slope is an independent risk factor of anterior cruciate ligament reconstruction graft rupture irrespective of graft choice.

INTRODUCTION: Anterior cruciate ligament (ACL) reconstruction failure remains a commonly seen complication despite advances in technique and graft options. Recently, several studies have shown that the inclination of the tibial plateau in the sagittal plane affects the stability of the knee joint. The purpose of this study was to determine if an increased posterior slope of the tibia is associated with failure of ACL reconstruction irrespective of the graft used. METHODS: From June 2002 to August 2003, a total of 100 patients with a symptomatic ACL-deficient knee were randomised to receive either a hamstring autograft or posterior tibialis allograft. All allografts were from a single tissue bank, aseptically processed, and fresh-frozen without terminal irradiation. ACL graft failures requiring reoperation with a minimum of 10-year follow-up were identified via telephone survey. Lateral radiographs of the knee of all patients were reviewed, and the slope of the tibia was measured using a standardised technique. Two fellowship-trained orthopaedic sports medicine specialists, one board-certified general orthopaedic surgeon, and two fellowship-trained musculoskeletal radiologists measured the tibial slope in all patients. RESULTS: At a minimum of 10-year follow-up, there were four (8.3%) autograft and 13 (26.5%) allograft failures that required revision reconstruction. The overall average tibial slope of the nonfailure cohort was 9.4°. The overall average tibial slope of the failure cohort was 11.9° (P â€‹= â€‹0.0002). The average slope of the allograft failures was 11.5°compared with an average slope of 9.6° in the nonfailures (P â€‹= â€‹0.01). The average slope of the autograft failures was 13.1° compared with 9.3° in the nonfailures (P â€‹= â€‹0.011). The mean difference in tibial slope measurements was 0.665 (95% confidence interval: 0.569-0.750). The interrater reliability, as measured by the intraclass correlation coefficient, for tibial slope was 0.898 (95% confidence interval: 0.859-0.928). The Cronbach α was 0.904. CONCLUSION: In a prospective, randomised trial of ACL reconstructions using either autograft or allograft, failures were associated with a significantly increased slope of the tibia compared with the nonfailures at 10-year follow-up.

Role of Order in the Mechanism of Charge Transport across Single-Stranded and Double-Stranded DNA Monolayers in Tunnel Junctions.

Deoxyribonucleic acid (DNA) has been hypothesized to act as a molecular wire due to the presence of an extended π-stack between base pairs, but the factors that are detrimental in the mechanism of charge transport (CT) across tunnel junctions with DNA are still unclear. Here we systematically investigate CT across dense DNA monolayers in large-area biomolecular tunnel junctions to determine when intrachain or interchain CT dominates and under which conditions the mechanism of CT becomes thermally activated. In our junctions, double-stranded DNA (dsDNA) is 30-fold more conductive than single-stranded DNA (ssDNA). The main reason for this large change in conductivity is that dsDNA forms ordered monolayers where intrachain tunneling dominates, resulting in high CT rates. By varying the temperature T and the length of the DNA fragments in the junctions, which determines the tunneling distance, we reveal a complex interplay between T, the length of DNA, and structural order on the mechanism of charge transport. Both the increase in the tunneling distance and the decrease in structural order result in a change in the mechanism of CT from coherent tunneling to incoherent tunneling (hopping). Our results highlight the importance of the interplay between structural order, tunneling distance, and temperature on the CT mechanism across DNA in molecular junctions.

Diverse, Potent, and Efficacious Inhibitors That Target the EED Subunit of the Polycomb Repressive Complex 2 Methyltransferase.

Aberrant activity of the histone methyltransferase polycomb repressive complex 2 (PRC2) has been linked to several cancers, with small-molecule inhibitors of the catalytic subunit of the PRC2 enhancer of zeste homologue 2 (EZH2) being recently approved for the treatment of epithelioid sarcoma (ES) and follicular lymphoma (FL). Compounds binding to the EED subunit of PRC2 have recently emerged as allosteric inhibitors of PRC2 methyltransferase activity. In contrast to orthosteric inhibitors that target EZH2, small molecules that bind to EED retain their efficacy in EZH2 inhibitor-resistant cell lines. In this paper we disclose the discovery of potent and orally bioavailable EED ligands with good solubilities. The solubility of the EED ligands was optimized through a variety of design tactics, with the resulting compounds exhibiting in vivo efficacy in EZH2-driven tumors.

Discovery of 5-{4-[(7-Ethyl-6-oxo-5,6-dihydro-1,5-naphthyridin-3-yl)methyl]piperazin-1-yl}-N-methylpyridine-2-carboxamide (AZD5305): A PARP1-DNA Trapper with High Selectivity for PARP1 over PARP2 and Other PARPs.

Poly-ADP-ribose-polymerase (PARP) inhibitors have achieved regulatory approval in oncology for homologous recombination repair deficient tumors including BRCA mutation. However, some have failed in combination with first-line chemotherapies, usually due to overlapping hematological toxicities. Currently approved PARP inhibitors lack selectivity for PARP1 over PARP2 and some other 16 PARP family members, and we hypothesized that this could contribute to toxicity. Recent literature has demonstrated that PARP1 inhibition and PARP1-DNA trapping are key for driving efficacy in a BRCA mutant background. Herein, we describe the structure- and property-based design of 25 (AZD5305), a potent and selective PARP1 inhibitor and PARP1-DNA trapper with excellent in vivo efficacy in a BRCA mutant HBCx-17 PDX model. Compound 25 is highly selective for PARP1 over other PARP family members, with good secondary pharmacology and physicochemical properties and excellent pharmacokinetics in preclinical species, with reduced effects on human bone marrow progenitor cells in vitro.

Recent Advances in Conventional Methods and Electrochemical Aptasensors for Mycotoxin Detection.

The presence of mycotoxins in foodstuffs and feedstuffs is a serious concern for human health. The detection of mycotoxins is therefore necessary as a preventive action to avoid the harmful contamination of foodstuffs and animal feed. In comparison with the considerable expense of treating contaminated foodstuffs, early detection is a cost-effective way to ensure food safety. The high affinity of bio-recognition molecules to mycotoxins has led to the development of affinity columns for sample pre-treatment and the development of biosensors for the quantitative analysis of mycotoxins. Aptamers are a very attractive class of biological receptors that are currently in great demand for the development of new biosensors. In this review, the improvement in the materials and methodology, and the working principles and performance of both conventional and recently developed methods are discussed. The key features and applications of the fundamental recognition elements, such as antibodies and aptamers are addressed. Recent advances in aptasensors that are based on different electrochemical (EC) transducers are reviewed in detail, especially from the perspective of the diagnostic mechanism; in addition, a brief introduction of some commercially available mycotoxin detection kits is provided.

Pyridones in drug discovery: Recent advances.

Pyridones have been utilized as privileged scaffolds in drug discovery. Some of the important roles where this class of heterocycles have found utility in medicinal chemistry include the ability to 1) serve both as a hydrogen bond acceptor and/or a donor; 2) act as a bioisostere for amides, phenyls, pyridines and other nitrogen- or oxygen-containing heterocycles; and 3) impact a target drug molecule's lipophilicity, aqueous solubility and metabolic stability. Detailed discussions of recent advances in their utilization as nonpeptidic mimics and as kinase hinge binding motifs are included. Selected literature examples published from the past twenty years where pyridones have been employed as bioisosteres for phenyls, pyridines, pyridine N-oxides and phenol rings are provided. In addition, this review summarizes the current understanding of possible reactive metabolites related to the pyridone structure.

Epitope-Specific Antibody Responses to a Plasmodium falciparum Subunit Vaccine Target in a Malaria-Endemic Population.

Circumsporozoite protein (CSP) coats the Plasmodium falciparum sporozoite surface and is a major malaria subunit vaccine target. We measured epitope-specific reactivity to field-derived CSP haplotypes in serum samples from Malian adults and children on a custom peptide microarray. Compared to children, adults showed greater antibody responses and responses to more variants in regions proximal to and within the central repeat region. Children acquired short-lived immunity to an epitope proximal to the central repeat region but not to the central repeat region itself. This approach has the potential to differentiate immunodominant from protective epitope-specific responses when combined with longitudinal infection data.

Microarray analyses reveal strain-specific antibody responses to Plasmodium falciparum apical membrane antigen 1 variants following natural infection and vaccination.

Vaccines based on Plasmodium falciparum apical membrane antigen 1 (AMA1) have failed due to extensive polymorphism in AMA1. To assess the strain-specificity of antibody responses to malaria infection and AMA1 vaccination, we designed protein and peptide microarrays representing hundreds of unique AMA1 variants. Following clinical malaria episodes, children had short-lived, sequence-independent increases in average whole-protein seroreactivity, as well as strain-specific responses to peptides representing diverse epitopes. Vaccination resulted in dramatically increased seroreactivity to all 263 AMA1 whole-protein variants. High-density peptide analysis revealed that vaccinated children had increases in seroreactivity to four distinct epitopes that exceeded responses to natural infection. A single amino acid change was critical to seroreactivity to peptides in a region of AMA1 associated with strain-specific vaccine efficacy. Antibody measurements using whole antigens may be biased towards conserved, immunodominant epitopes. Peptide microarrays may help to identify immunogenic epitopes, define correlates of vaccine protection, and measure strain-specific vaccine-induced antibodies.

Correction to "DNA Brush-Directed Vertical Alignment of Extensive Gold Nanorod Arrays with Controlled Density".

[This corrects the article DOI: 10.1021/acsomega.7b00303.].

Antibodies to Peptides in Semiconserved Domains of RIFINs and STEVORs Correlate with Malaria Exposure.

The repetitive interspersed family (RIFIN) and the subtelomeric variable open reading frame (STEVOR) family represent two of three major Plasmodium falciparum variant surface antigen families involved in malaria pathogenesis and immune evasion and are potential targets in the development of natural immunity. Protein and peptide microarrays populated with RIFINs and STEVORs associated with severe malaria vulnerability in Malian children were probed with adult and pediatric sera to identify epitopes that reflect malaria exposure. Adult sera recognized and reacted with greater intensity to all STEVOR proteins than pediatric sera did. Serorecognition of and seroreactivity to peptides within the semiconserved domain of STEVORs increased with age and seasonal malaria exposure, while serorecognition and seroreactivity increased for the semiconserved and second hypervariable domains of RIFINs only with age. Serologic responses to RIFIN and STEVOR peptides within the semiconserved domains may play a role in natural immunity to severe malaria.IMPORTANCE Malaria, an infectious disease caused by the parasite Plasmodium falciparum, causes nearly 435,000 deaths annually worldwide. RIFINs and STEVORs are two variant surface antigen families that are involved in malaria pathogenesis and immune evasion. Recent work has shown that a lack of humoral immunity to these proteins is associated with severe malaria vulnerability in Malian children. This is the first study to have compared serologic responses of children and adults to RIFINs and STEVORs in settings of malaria endemicity and to examine such serologic responses before and after a clinical malaria episode. Using microarrays, we determined that the semiconserved domains in these two parasite variant surface antigen families harbor peptides whose seroreactivity reflects malaria exposure. A similar approach has the potential to illuminate the role of variant surface antigens in the development of natural immunity to clinical malaria. Potential vaccines for severe malaria should include consideration of peptides within the semiconserved domains of RIFINs and STEVORs.

Meniscal and Chondral Pathology Associated With Anterior Cruciate Ligament Injuries.

Anterior cruciate ligament (ACL) ruptures are commonly associated with meniscal and articular cartilage injuries, and the presence of these defects influences both short- and long-term outcomes. Multiple variables are predictive of this pathology including time from injury, age, and sex. Revision ACL reconstructions demonstrate higher rates of chondral injury than primary reconstructions. Menisci are important secondary stabilizers of the knee in the setting of ACL deficiency, and specific tear types are more consistently associated with ACL injury. Successful outcomes with multiple treatment options for meniscal tears in conjunction with ACL reconstruction have been reported. Maintaining meniscal integrity may be protective of both joint surfaces and graft stability in the long term; however, clear treatment recommendations for tear subtypes remain ill defined. High-grade chondral defects have the most consistent and potentially largest negative effect on long-term patient-reported outcomes; however, optimal treatment is also controversial with successful results demonstrated with several modalities including benign neglect.

Physiology of Hyperuricemia and Urate-Lowering Treatments.

Gout is the most common form of inflammatory arthritis and is a multifactorial disease typically characterized by hyperuricemia and monosodium urate crystal deposition predominantly in, but not limited to, the joints and the urinary tract. The prevalence of gout and hyperuricemia has increased in developed countries over the past two decades and research into the area has become progressively more active. We review the current field of knowledge with emphasis on active areas of hyperuricemia research including the underlying physiology, genetics and epidemiology, with a focus on studies which suggest association of hyperuricemia with common comorbidities including cardiovascular disease, renal insufficiency, metabolic syndrome and diabetes. Finally, we discuss current therapies and emerging drug discovery efforts aimed at delivering an optimized clinical treatment strategy.

The Synthesis of Designer DNA.

The synthesis of designer DNA requires an approach where the user can determine both the sequence and the number of nucleobases. The protocol outlined here describes an enzymatic method for the synthesis of long repeat-sequence DNA. The method utilizes a PCR-based approach; starting with short oligo-seeds, c.a. 20 bp, bearing a minimum of two repeating units of >8 bp sequences. During each heat-cool cycle, the oligo-seeds reanneal imperfectly leaving an overhang, which is then extended by the polymerase. The final length of the DNA is determined by the number of heat-cool cycles performed, reaching up to 20,000 bp after 20 cycles.