The distribution and antibiotic-resistant characteristics and risk factors of pathogens associated with clinical biliary tract infection in humans.

Introduction: Biliary Infection in patients is a common and important phenomenon resulting in severe complications and high morbidity, while the distributions and drug resistance profiles of biliary bacteria and related risk factors are dynamic. This study explored the characteristics of and risk factors for biliary infection to promote the rational use of antibiotics in clinically. Methods: Bacterial identification and drug susceptibility testing were completed using the Vitek 2 Compact analysis system. The distribution and antibiotic-resistant characteristics of 3,490 strains of biliary bacteria in patients at Nankai Hospital from 2019 to 2021 were analyzed using Whonet 5.6 and SPSS 26.0 software. We then retrospectively analyzed the clinical data and risk factors associated with 2,340 strains of Gram-negative bacilli, which were divided into multidrug-resistant bacteria (1,508 cases) and non-multidrug-resistant bacteria (832 cases) by a multivariate Cox regression model. Results and discussion: A total of 3,490 pathogenic bacterial strains were isolated from bile samples, including 2,340 (67.05%) Gram-negative strains, 1,029 (29.48%) Gram-positive strains, and 109 (4.56%) fungal strains. The top five pathogenic bacteria were Escherichia coli, Klebsiella pneumoniae, Enterococcus faecium, Enterococcus faecalis, and Pseudomonas aeruginosa. The rate of Escherichia coli resistance to ciprofloxacin increased (p < 0.05), while the resistance to amikacin decreased (p < 0.05). The resistance of Klebsiella pneumoniae to cephalosporins, carbapenems, ß-lactamase inhibitors, cephalases, aminoglycosides, and quinolones increased (p < 0.05), and the resistance of Pseudomonas aeruginosa to piperacillin, piperacillin/tazobactam, ticacillin/clavulanic acid, and amicacin declined significantly (p < 0.05). The resistance of Enterococcus faecium to tetracycline increased by year (p < 0.05), and the resistance of Enterococcus faecalis to erythromycin and high-concentration gentamicin declined (p < 0.05). Multivariate logistic regression analysis suggested that the administration of third- or fourth-generation cephalosporins was an independent risk factor for biliary infection. In summary, Gram-negative bacilli were the most common pathogenic bacteria isolated from biliary infection patients, especially Escherichia coli, and the rates and patterns of drug resistance were high and in constant flux; therefore, rational antimicrobial drug use should be carried out considering risk factors.

Are children with IgA nephropathy different from adult patients?

BACKGROUND: Previously, several studies have indicated that pediatric IgA nephropathy (IgAN) might be different from adult IgAN, and treatment strategies might be also different between pediatric IgAN and adult IgAN. METHODS: We analyzed two prospective cohorts established by pediatric and adult nephrologists, respectively. A comprehensive analysis was performed investigating the difference in clinical and pathological characteristics, treatment, and prognosis between children and adults with IgAN. RESULTS: A total of 1015 children and 1911 adults with IgAN were eligible for analysis. More frequent gross hematuria (88% vs. 20%, p < 0.0001) and higher proteinuria (1.8 vs. 1.3 g/d, p < 0.0001) were seen in children compared to adults. In comparison, the estimated glomerular filtration rate (eGFR) was lower in adults (80.4 vs. 163 ml/min/1.73 m2, p < 0.0001). Hypertension was more prevalent in adult patients. Pathologically, a higher proportion of M1 was revealed (62% vs. 39%, p < 0.0001) in children than in adults. S1 (62% vs. 28%, p < 0.0001) and T1-2 (34% vs. 8%, p < 0.0001) were more frequent in adults. Adjusted by proteinuria, eGFR, and hypertension, children were more likely to be treated with glucocorticoids than adults (87% vs. 45%, p < 0.0001). After propensity score matching, in IgAN with proteinuria > 1 g/d, children treated with steroids were 1.87 (95% CI 1.16-3.02, p = 0.01) times more likely to reach complete remission of proteinuria compared with adults treated with steroids. CONCLUSIONS: Children present significantly differently from adults with IgAN in clinical and pathological manifestations and disease progression. Steroid response might be better in children.

TsImpute: an accurate two-step imputation method for single-cell RNA-seq data.

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) technology has enabled discovering gene expression patterns at single cell resolution. However, due to technical limitations, there are usually excessive zeros, called "dropouts," in scRNA-seq data, which may mislead the downstream analysis. Therefore, it is crucial to impute these dropouts to recover the biological information. RESULTS: We propose a two-step imputation method called tsImpute to impute scRNA-seq data. At the first step, tsImpute adopts zero-inflated negative binomial distribution to discriminate dropouts from true zeros and performs initial imputation by calculating the expected expression level. At the second step, it conducts clustering with this modified expression matrix, based on which the final distance weighted imputation is performed. Numerical results based on both simulated and real data show that tsImpute achieves favorable performance in terms of gene expression recovery, cell clustering, and differential expression analysis. AVAILABILITY AND IMPLEMENTATION: The R package of tsImpute is available at https://github.com/ZhengWeihuaYNU/tsImpute.

Different Physiological Responses to Continuous Drought between Seedlings and Younger Individuals of Haloxylon ammodendron.

Drought is an important environmental factor that influences physiological processes in plants; however, few studies have examined the physiological mechanisms underlying plants' responses to continuous drought. In this study, the seedlings and younger individuals of Haloxylon ammodendron were experimentally planted in the southern part of the Gurbantunggut Desert. We measured their photosynthetic traits, functional traits and non-structural carbohydrate contents (NSCs) in order to assess the effects of continuous drought (at 15-day and 30-day drought points) on the plants' physiological responses. The results showed that at the 15-day (15 d) drought point, the leaf light-saturated net photosynthetic rate (An) values of both the seedlings and the younger individuals were decreased (by -68.9% and -45.2%, respectively). The intrinsic water use efficiency (iWUE) of the seedlings was significantly lower than that of the control group (-52.2%), but there was no diffenrence of iWUE observed in younger individuals. At the 30-day (30 d) drought point, a decrease in the An (-129.8%) of the seedlings was induced via biochemical inhibition, with a lower potential maximum photochemical rate (Fv/Fm, 0.42) compared with the control group, while a decrease in the An (-52.3%) of the younger individuals was induced due to lower stomatal conductance (gs, -50.5%). Our results indicated that prolonged drought induced a greater risk of seedling mortality as the relatively limited ability of stomatal regulation may increase the possibility of massive embolism, resulting in hydraulic failure.

Squamous cell carcinoma of the cystic duct: A case report and literature review.

RATIONALE: Pure squamous cell carcinoma (SCC) of the gallbladder is a rare malignant biliary tract tumor predominantly found in the body and neck of the gallbladder. However, its occurrence in the cystic duct is even rarer. Given its rarity, no established guidelines or consensus currently exist regarding the treatment of pure SCC of the gallbladder. We report an unusual case of SCC originating from the cystic duct with the intent of providing insights into the therapeutic approach for this type of malignancy. PATIENT CONCERNS: A male patient presented to our hospital with acute cholecystitis. Unexpectedly, imaging revealed gallbladder malignancy. DIAGNOSES: Pathologic examination after surgery confirmed SCC of the cystic duct. INTERVENTIONS: Despite elevated bilirubin levels, we were able to exclude hilar involvement, enabling radical tumor resection. Intraoperatively, we discovered that the tumor was located in the cystic duct, a site associated with a high likelihood of invasion into neighboring organs. The tumor demonstrated a predominantly exophytic growth pattern, which prompted us to refrain from extending the resection range, thereby striking a balance between complete tumor removal and surgical trauma. We performed liver wedge resection only to ensure a negative resection margin while preserving the anatomical structure to the greatest extent possible. Postoperative recovery was rapid and uncomplicated. Pathological examination confirmed pure SCC, which led us to initiate a regimen of nab-paclitaxel and cisplatin, which is known to be effective in other organ SCCs. Remarkably, the patient experienced a rare and severe posttreatment cardiovascular event. Consequently, we switched the patient to a chemotherapy regimen of gemcitabine and cisplatin, which ultimately yielded positive clinical outcomes. OUTCOMES: no evidence of tumor recurrence was observed within 1 year after surgery. LESSONS: The diagnosis and therapeutic strategy for rare tumors such as gallbladder SCC should be meticulously tailored based on their unique characteristics to optimize postoperative patient outcomes.

Multi-dimensional search for drug-target interaction prediction by preserving the consistency of attention distribution.

Predicting drug-target interaction (DTI) is a crucial step in the process of drug repurposing and new drug development. Although the attention mechanism has been widely used to capture the interactions between drugs and targets, it mainly uses the Simplified Molecular Input Line Entry System (SMILES) and two-dimensional (2D) molecular graph features of drugs. In this paper, we propose a neural network model called MdDTI for DTI prediction. The model searches for binding sites that may interact with the target from the multiple dimensions of drug structure, namely the 2D substructures and the three-dimensional (3D) spatial structure. For the 2D substructures, we have developed a novel substructure decomposition strategy based on drug molecular graphs and compared its performance with the SMILES-based decomposition method. For the 3D spatial structure of drugs, we constructed spatial feature representation matrices for drugs based on the Cartesian coordinates of heavy atoms (without hydrogen atoms) in each drug. Finally, to ensure the search results of the model are consistent across multiple dimensions, we construct a consistency loss function. We evaluate MdDTI on four drug-target interaction datasets and three independent compound-protein affinity test sets. The results indicate that our model surpasses a series of state-of-the-art models. Case studies demonstrate that our model is capable of capturing the potential binding regions between drugs and targets, and it shows efficacy in drug repurposing. Our code is available at https://github.com/lhhu1999/MdDTI.

EIU-Net: Enhanced feature extraction and improved skip connections in U-Net for skin lesion segmentation.

Skin lesion segmentation is a computer-aided diagnosis method for quantitative analysis of melanoma that can improve efficiency and accuracy. Although many methods based on U-Net have achieved tremendous success, they still cannot handle challenging tasks well due to weak feature extraction. In response to skin lesion segmentation, a novel method called EIU-Net is proposed to tackle the challenging task. To capture the local and global contextual information, we employ inverted residual blocks and an efficient pyramid squeeze attention (EPSA) block as the main encoders at different stages, while atrous spatial pyramid pooling (ASPP) is utilized after the last encoder and the soft-pool method is introduced for downsampling. Also, we propose a novel method named multi-layer fusion (MLF) module to effectively fuse the feature distributions and capture significant boundary information of skin lesions in different encoders to improve the performance of the network. Furthermore, a reshaped decoders fusion module is used to obtain multi-scale information by fusing feature maps of different decoders to improve the final results of skin lesion segmentation. To validate the performance of our proposed network, we compare it with other methods on four public datasets, including the ISIC 2016, ISIC 2017, ISIC 2018, and PH2 datasets. And the main metric Dice scores achieved by our proposed EIU-Net are 0.919, 0.855, 0.902, and 0.916 on the four datasets, respectively, outperforming other methods. Ablation experiments also demonstrate the effectiveness of the main modules in our proposed network. Our code is available at https://github.com/AwebNoob/EIU-Net.

TRIM5α recruits HDAC1 to p50 and Sp1 and promotes H3K9 deacetylation at the HIV-1 LTR.

Tripartite motif-containing protein 5α (TRIM5α) is generally known to block the postentry events of HIV-1. Here, we report an uncharacterized role for TRIM5α in the maintenance of viral latency. Knockdown of TRIM5α potentiates the transcription of HIV-1 in multiple latency models, which is reversed by shRNA-resistant TRIM5α. TRIM5α suppresses TNFα-activated HIV-1 LTR-driven as well as NF-κB- and Sp1-driven gene expression, with the RING and B-box 2 domains being the essential determinants. Mechanistically, TRIM5α binds to and enhances the recruitment of histone deacetylase 1 (HDAC1) to NF-κB p50 and Sp1. ChIP‒qPCR analyses further reveal that the association of TRIM5α with HIV-1 LTR induces HDAC1 recruitment and local H3K9 deacetylation. Conserved suppression effects of TRIM5α orthologs from multiple species on both HIV-1 and endo-retroelement HERV-K LTR activities have also been demonstrated. These findings provide new insights into the molecular mechanisms by which proviral latency is initially established and activatable proviruses are resilenced by histone deacetylase recruitment.

Working Condition Recognition Based on Transfer Learning and Attention Mechanism for a Rotary Kiln.

It is difficult to identify the working conditions of the rotary kilns due to the harsh environment in the kilns. The flame images of the firing zone in the kilns contain a lot of working condition information, but the flame image data sample size is too small to be used to fully extract the key features. In order to solve this problem, a method combining transfer learning and attention mechanism is proposed to extract key features of flame images, in which the deep residual network is used as the backbone network, the coordinate attention module is introduced to capture the position information and channel information on the branch of feature graphs, and the features of flame images obtained are further screened to improve the extraction ability. At the same time, migration learning is performed by the pre-trained ImageNet data set, and feature migration and parameter sharing are realized to cope with the training difficulty of a small sample data size. Moreover, an activation function Mish is introduced to reduce the loss of effective information. The experimental results show that, compared with traditional methods, the working condition recognition accuracy of rotary kilns is improved by about 5% with the proposed method.

Case Report: Successful treatment of severe pneumocystis carinii pneumonia in a case series of primary nephrotic syndrome after receiving anti-CD20 monoclonal antibody therapy.

Rituximab is emerging as a new steroid sparing agent in children with difficult-to-treat nephrotic syndrome due to its ability of depleting CD20-positive B cells. Life-threatening adverse events such as pneumocystis carinii pneumonia may occur even though it seems to be well tolerated. Since rituximab is wildly used in immune-mediated diseases, it is important to manage its severe adverse events. To explore the importance of early diagnosis and treatment of pneumocystis carinii pneumonia in children with primary nephrotic syndrome (PNS) after receiving rituximab therapy, we retrospectively analyzed the clinical data of PNS patients younger than 18 years old with pneumocystis carinii pneumonia who were hospitalized in our center. Clinical features and laboratory test results were retrieved from the electronic medical records. Severe pneumocystis carinii pneumonia occurred in one child with steroid resistant nephrotic syndrome and two with steroid dependent nephrotic syndrome patients after rituximab treatment. These patients were diagnosed in time by metagenomic next-generation sequencing (mNGS) for pathogen detection. Fortunately, all three patients survived after antifungal treatment and achieved complete remission eventually. In conclusion, early diagnosis by using mNGS and timely antifungal treatment is the key to successful management of pneumocystis carinii pneumonia in children with difficult-to-treat PNS.

Successful totally laparoscopic right trihepatectomy following conversion therapy for hepatocellular carcinoma: A case report.

BACKGROUND: About 20%-30% of newly diagnosed hepatocellular carcinoma (HCC) patients are surgically feasible due to a variety of reasons. Active conversion therapy may provide opportunities of surgery for these patients. Nevertheless, the choice of surgical procedure is controversial after successful conversion therapy. We report a patient with HCC who underwent successful laparoscopic right trisectionectomy after conversion therapy with portal vein embolization and transarterial chemoembolization. CASE SUMMARY: A 67-year-old male patient presented to our hospital with epigastric distention/ discomfort and nausea/vomiting for more than 1 mo. Contrast-enhanced computed tomography scan of the abdomen demonstrated multiple tumors (the largest was ≥ 10 cm in diameter) located in the right liver and left medial lobe, and the left lateral lobe was normal. The future remnant liver (FRL) of the left lateral lobe accounted for only 18% of total liver volume after virtual resection on the three-dimensional liver model. Conversion therapy was adopted after orally administered entecavir for antiviral treatment. First, the right portal vein was embolized. Then tumor embolization was performed via the variant hepatic arteries. After 3 wk, the FRL of the left lateral lobe accounted for nearly 30% of the total liver volume. Totally laparoscopic right trisectionectomy was performed under combined epidural and general anesthesia. The in situ resection was performed via an anterior approach. The operating time was 240 min. No clamping was required during the surgery, and the intraoperative blood loss was 300 mL. There were no postoperative complications such as bile leakage, and the incision healed well. The patient was discharged on the 8th postoperative day. During the 3-mo follow-up, there was no recurrence and obvious hyperplasia of residual liver was observed. Alpha-fetoprotein decreased significantly and tended to be normal. CONCLUSION: Due to the different biological characteristics of the liver cancer and the pathophysiological features of the liver from other organs, the conversion treatment should take into account both the feasibility of tumor downstaging and the volume and function of the remnant liver. Our case provides a reference for clinicians in terms of both conversion therapy and laparoscopic right trisectionectomy.

Effects of Polydopamine Microspheres Loaded with Silver Nanoparticles on Lolium multiflorum: Bigger Size, Less Toxic.

The rapid development of nanotechnology and its widespread use have given rise to serious concerns over the potential adverse impacts of nanomaterials on the Earth's ecosystems. Among all the nanomaterials, silver nanoparticles (AgNPs) are one of the most extensively used nanomaterials due to their excellent antibacterial property. However, the toxic mechanism of AgNPs in nature is still unclear. One of the questions under debate is whether the toxicity is associated with the size of AgNPs or the silver ions released from AgNPs. In our previous study, a sub-micron hybrid sphere system with polydopamine-stabilized AgNPs (Ag@PDS) was synthesized through a facile and green method, exhibiting superior antibacterial properties. The current study aims to explore the unique toxicity profile of this hybrid sphere system by studying its effect on germination and early growth of Lolium multiflorum, with AgNO3 and 15 nm AgNPs as a comparison. The results showed the seed germination was insensitive/less sensitive to all three reagents; however, vegetative growth was more sensitive. Specifically, when the Ag concentration was lower than 40 mg/L, Ag@PDS almost had no adverse effects on the root and shoot growth of Lolium multiflorum seeds. By contrast, when treated with AgNO3 at a lower Ag concentration of 5 mg/L, the plant growth was inhibited significantly, and was reduced more in the case of AgNP treatment at the same Ag concentration. As the exposures of Ag@PDS, AgNO3, and AgNPs increased, so did the Ag content in the root and shoot. In general, Ag@PDS was proven to be a potential useful hybrid material that retains antibacterial property with light phytotoxicity.

Design of a free-form surface microlens array optical system with high efficiency and uniformity.

The microlens array has been widely applied in LED lighting source due to its special optical properties, but most of the research lacks the analysis and optimization of the complete mathematical models. Hence, the new design method of a free-form surface microlens array optical system is proposed in this paper. Based on the characteristics of TIR and the law of refraction, a complete mathematical model of the free-form microlens is established. By numerically solving a set of differential equations, the profile of the free-form surface microlens is obtained. Then we rotate the profile to get the free-form surface microlens. Finally, the proposed microlens array is simulated and analyzed in near-field and far-field situations, respectively. We also discuss the influence of microlens array characteristics on illumination performance. The result shows the uniformity and efficiency have been improved, both of which can reach more than 90%.

LINC00346 promotes hepatocellular carcinoma progression via activating the JAK-STAT3 signaling pathway.

Hepatocellular carcinoma (HCC) remains the most common malignant tumor worldwide. Long noncoding RNAs can modulate various tumorigenic processes. In addition, growing evidence has indicated tha the Janus kinase-signal transducer and activator of transcription (JAK-STAT) pathway is activated in multiple cancers, including HCC. Recently, it was found that LINC00346 can participate in several cancers. Nevertheless, the biological roles of LINC00346 in HCC have been barely investigated. In this study, the function of LINC00346 was specifically concentrated upon. We observed that LINC00346 was obviously elevated in HCC cells (Bel7404, Huh-6, HepG2, and QGY-7703 cells). Then, Bel7404 and HepG2 cells were overexpressed with LINC00346. Overexpression of LINC00346 repressed HCC cell survival and cell proliferation. In addition, apoptosis of Bel7404 and HepG2 cells was triggered by LINC00346 upregulation. Bel7404 and HepG2 cell cycle was arrested in the G1 phase by LINC00346. Meanwhile, we conducted wound-healing assay and Transwell invasion assays. As shown, we observed that the migratory and invasive capacities of Bel7404 and HepG2 cells were remarkably restrained by the increase of LINC00346. Moreover, we showed that LINC00346 overexpression activated the JAK-STAT3 pathway, which is involved in many cancers. Afterward, in vivo experiments were utilized and we proved that LINC00346 was able to induce HCC tumor growth via activating the JAK-STAT3 pathway. To conclude, we revealed the potential possibility of developing LINC00346 as an indicator for HCC.

Multiple Binding Configurations of Fis Protein Pairs on DNA: Facilitated Dissociation versus Cooperative Dissociation.

As a master transcription regulator, the Fis protein influences over two hundred genes of E. coli. The Fis protein's nonspecific binding to DNA is widely acknowledged, and its kinetics of dissociation from DNA is strongly influenced by its surroundings: the dissociation rate increases as the concentration of the Fis protein in the solution phase increases. In this study, we use computational methods to explore the global binding energy landscape of the Fis1:Fis2:DNA ternary complex. The complex contains a binary-Fis molecular dyad whose formation relies on complex structural rearrangements. The simulations allow us to distinguish several different pathways for the dissociation of the protein from DNA with different functional outcomes and involving different protein stoichiometries: (1) simple exchange of proteins and (2) cooperative unbinding of two Fis proteins to yield bare DNA. In the case of exchange, the protein on the DNA is replaced by the solution-phase protein through competition for DNA binding sites. This process seen in fluorescence imaging experiments has been called facilitated dissociation. In the latter case of cooperative unbinding of pairs, two neighboring Fis proteins on DNA form a unique binary-Fis configuration via protein-protein interactions, which in turn leads to the codissociation of both molecules simultaneously, a process akin to the "molecular stripping" seen in the NFκB/IκB genetic broadcasting system. This simulation shows that the existence of multiple binding configurations of transcription factors can have a significant impact on the kinetics and outcome of transcription factor dissociation from DNA, with important implications for the systems biology of gene regulation by Fis.

Effects of natural and modified calcium-based sorbents on heavy metals of food waste under oxy-fuel combustion.

Performance of natural and modified calcium-based sorbents for heavy metals for food waste under oxy-fuel combustion in a lab-scale tubular furnace was carried out. The effects of furnace temperature, sorbents type, and CO2/O2 ratio on adsorption of heavy metals were investigated. Increasing the furnace temperature helped fixing Al in the bottom ash, but increased the volatilization of Zn. The results showed that heavy metals captured by sorbents highly depended on the metals types. Nature and modified CaO had excellent performance for Al capture while CaCO3 could not absorb Al. Neither CaCO3 or CaO could not use as sorbents for the Cr capture. CO2/O2 ratio highly affected the capture of Cr and Zn but had no influence on Al, and the decrease of CO2/O2 ratio would help capturing Cr and Zn. This work contributes to the heavy metals controlled by Ca-based sorbents during municipal solid waste oxy-fuel combustion.

Poly(3,6-diamino-9-ethylcarbazole) based molecularly imprinted polymer sensor for ultra-sensitive and selective detection of 17-ß-estradiol in biological fluids.

In this work, we reported the synthesis of 3, 6-diamino-9-ethylcarbazole and its application as a new monomer for preparation of molecularly imprinted polymer (MIP) electrochemical sensor. The as prepared MIP sensor exhibited ultrahigh sensitivity and selectivity for the detection of 17-ß-estradiol in attomolar levels (1 × 10-18molL-1). The sensor works by detecting the change of the interfacial impedance that is derived from recognition of 17-ß-estradiol on the MIP layer. The MIP sensor based on 3, 6-diamino-9-ethylcarbazole monomer revealed better performance than that of unmodified carbazole monomer. The monomer/template ratio, electropolymerization scanning cycles, and the incubation pH values were optimised in order to obtain the best detection efficiency. Under the optimised condition, the MIP sensor exhibits a wide linear range from 1aM to 10µM (1 × 10-18 ̶ 1 × 10-5molL-1). A low detection limit of 0.36aM (3.6 × 10-19molL-1) and a good selectivity towards structurally similar compounds were obtained. The proposed MIP sensor also exhibits long-term stability and applicability in human serum samples. These advantages enabled this MIP sensor to be a promising alternative of electrochemical sensor and may be extended to detection of other endogenous compounds.

The Associative Memory, Water Mediated, Structure and Energy Model (AWSEM)-Amylometer: Predicting Amyloid Propensity and Fibril Topology Using an Optimized Folding Landscape Model.

Amyloids are fibrillar protein aggregates with simple repeated structural motifs in their cores, usually ß-strands but sometimes α-helices. Identifying the amyloid-prone regions within protein sequences is important both for understanding the mechanisms of amyloid-associated diseases and for understanding functional amyloids. Based on the crystal structures of seven cross-ß amyloidogenic peptides with different topologies and one recently solved cross-α fiber structure, we have developed a computational approach for identifying amyloidogenic segments in protein sequences using the Associative memory, Water mediated, Structure and Energy Model (AWSEM). The AWSEM-Amylometer performs favorably in comparison with other predictors in predicting aggregation-prone sequences in multiple data sets. The method also predicts well the specific topologies (the relative arrangement of ß-strands in the core) of the amyloid fibrils. An important advantage of the AWSEM-Amylometer over other existing methods is its direct connection with an efficient, optimized protein folding simulation model, AWSEM. This connection allows one to combine efficient and accurate search of protein sequences for amyloidogenic segments with the detailed study of the thermodynamic and kinetic roles that these segments play in folding and aggregation in the context of the entire protein sequence. We present new simulation results that highlight the free energy landscapes of peptides that can take on multiple fibril topologies. We also demonstrate how the Amylometer methodology can be straightforwardly extended to the study of functional amyloids that have the recently discovered cross-α fibril architecture.

Resolving the NFκB Heterodimer Binding Paradox: Strain and Frustration Guide the Binding of Dimeric Transcription Factors.

Many eukaryotic transcription factors function after forming oligomers. The choice of protein partners is a nonrandom event that has distinct functional consequences for gene regulation. In the present work we examine three dimers of transcription factors in the NFκB family: p50p50, p50p65, and p65p65. The NFκB dimers bind to a myriad of genomic sites and switch the targeted genes on or off with precision. The p65p50 heterodimer of NFκB is the strongest DNA binder, and its unbinding is controlled kinetically by molecular stripping from the DNA induced by IκB. In contrast, the homodimeric forms of NFκB, p50p50 and p65p65, bind DNA with significantly less affinity, which places the DNA residence of the homodimers under thermodynamic rather than kinetic control. It seems paradoxical that the heterodimer should bind more strongly than either of the symmetric homodimers since DNA is a nearly symmetric target. Using a variety of energy landscape analysis tools, here we uncover the features in the molecular architecture of NFκB dimers that are responsible for these drastically different binding free energies. We show that frustration in the heterodimer interface gives the heterodimer greater conformational plasticity, allowing the heterodimer to better accommodate the DNA. We also show how the elastic energy and mechanical strain in NFκB dimers can be found by extracting the principal components of the fluctuations in Cartesian coordinates as well as fluctuations in the space of physical contacts, which are sampled via simulations with a predictive energy landscape Hamiltonian. These energetic contributions determine the specific detailed mechanisms of binding and stripping for both homo- and heterodimers.