Regeneration of the human segmentation clock in somitoids in vitro

Each vertebrate species appears to have a unique timing mechanism for forming somites along the vertebral column, and the process in human remains poorly understood at the molecular level due to technical and ethical limitations. Here, we report the reconstitution of human segmentation clock by direct reprogramming. We first reprogrammed human urine epithelial cells to a presomitic mesoderm (PSM) state capable of long-term self-renewal and formation of somitoids with an anterior-to-posterior axis. By inserting the RNA reporter Pepper into HES7 and MESP2 loci of these iPSM cells, we show that both transcripts oscillate in the resulting somitoids at ~5 h/cycle. GFP-tagged endogenous HES7 protein moves along the anterior-to-posterior axis during somitoid formation. The geo-sequencing analysis further confirmed anterior-to-posterior polarity and revealed the localized expression of WNT, BMP, FGF, and RA signaling molecules and HOXA-D family members. Our study demonstrates the direct reconstitution of human segmentation clock from somatic cells, which may allow future dissection of the mechanism and components of such a clock and aid regenerative medicine.

Generation of mitochondria-rich kidney organoids from expandable intermediate mesoderm progenitors reprogrammed from human urine cells under defined medium

BACKGROUND

The kidneys require vast amounts of mitochondria to provide ample energy to reabsorb nutrients and regulate electrolyte, fluid, and blood pressure homeostasis. The lack of the human model hinders the investigation of mitochondria homeostasis related to kidney physiology and disease.

RESULTS

Here, we report the generation of mitochondria-rich kidney organoids via partial reprogramming of human urine cells (hUCs) under the defined medium. First, we reprogrammed mitochondria-rich hUCs into expandable intermediate mesoderm progenitor like cells (U-iIMPLCs), which in turn generated nephron progenitors and formed kidney organoids in both 2D and 3D cultures. Cell fate transitions were confirmed at each stage by marker expressions at the RNA and protein levels, along with chromatin accessibility dynamics. Single cell RNA-seq revealed hUCs-induced kidney organoids (U-iKOs) consist of podocytes, tubules, and mesenchyme cells with 2D dominated with mesenchyme and 3D with tubule and enriched specific mitochondria function associated genes. Specific cell types, such as podocytes and proximal tubules, loop of Henle, and distal tubules, were readily identified. Consistent with these cell types, 3D organoids exhibited the functional and structural features of the kidney, as indicated by dextran uptake and transmission electron microscopy. These organoids can be further matured in the chick chorioallantoic membrane. Finally, cisplatin, gentamicin, and forskolin treatment led to anatomical abnormalities typical of kidney injury and altered mitochondria homeostasis respectively.

CONCLUSIONS

Our study demonstrates that U-iKOs recapitulate the structural and functional characteristics of the kidneys, providing a promising model to study mitochondria-related kidney physiology and disease in a personalized manner.

Appropriate Exogenous Expression Stoichiometry of GATA4 as an Important Factor for Cardiac Reprogramming of Human Dermal Fibroblasts

Reprogramming of human dermal fibroblasts (HDFs) into induced cardiomyocyte-like cells (iCMs) represents a promising strategy for human cardiac regeneration. Different cocktails of cardiac transcription factors can convert HDFs into iCMs, although with low efficiency and immature phenotype. Here, GATA4, MEF2C, TBX5, MESP1, and MYOCD (GMTMeMy for short) were used to reprogram HDFs by retrovirus infection. We found that the exogenous expression stoichiometry of GATA4 (GATA4 stoichiometry) significantly affected reprogramming efficiency. When 1/8 dosage of GATA4 virus (GATA4 dosage) plus MTMeMy was used, the reprogramming efficiency was obviously improved compared with average pooled virus encoding each factor, which measured, by the expression level of cardiac genes, the percentage of cardiac troponin T and alpha-cardiac myosin heavy-chain immunopositive cells and the numbers of iCMs showing calcium oscillation or beating synchronously in co-culture with mouse CMs. In addition, we prepared conditioned maintenance medium (CMM) by CM differentiation of H9 human embryonic stem cell line. We found that compared with traditional maintenance medium (TMM), CMM made iCMs show well-organized sarcomere formation and characteristic calcium oscillation wave earlier. These findings demonstrated that appropriate GATA4 stoichiometry was essential for cardiac reprogramming and some components in CMM were important for maturation of iCMs.

MYOCD is Required for Cardiomyocyte-like Cells Induction from Human Urine Cells and Fibroblasts Through Remodeling Chromatin

Despite direct reprogramming of human cardiac fibroblasts into induced cardiomyocytes (iCM) holds great potential for heart regeneration, the mechanisms are poorly understood. Whether other human somatic cells could be reprogrammed into cardiomyocytes is also unknown. Here, we report human urine cells (hUCs) could be converted into CM-like cells from different donors and the related chromatin accessibility dynamics (CAD) by assay for transposase accessible chromatin(ATAC)-seq. hUCs transduced by MEF2C, TBX5, MESP1 and MYOCD but without GATA4 expressed multiple cardiac specific genes, exhibited Ca²⁺ oscillation potential and sarcomeric structures, and contracted synchronously in coculture with mouse CM. Additionally, we found that MYOCD is required for both closing and opening critical loci, mainly by hindering the opening of loci enriched with motifs for the TEAD and AP1 family and promoting the closing of loci enriched with ETS motifs. These changes differ partially from CAD observed during iCM induction from human fibroblasts. Collectively, our study offers one practical platform for iCM generation and insights into mechanisms for iCM fate determination.

EGFR testing patterns and detection of EGFR exon 20 insertions among patients with NSCLC in the US

Introduction/Objective

Epidermal growth factor receptor (EGFR) mutations are common in non-small cell lung cancer (NSCLC). EGFR exon 20 insertions (EGFRex20ins), a rare subset of EGFR mutations, are refractory to tyrosine kinase inhibitors. With the development of targeted therapies for EGFRex20ins, such as mobocertinib, molecular testing is required to optimize treatment. A better understanding of real-world EGFR detection patterns is needed to maximize patient outcomes.

Methods/Case Report

This retrospective study describes EGFR testing and EGFRex20ins detection patterns in patients with NSCLC in the United States. The Flatiron Health electronic health record database was used to identify patients ≥18 years, with advanced NSCLC, and with ≥2 clinic visits between 01/01/2011 and 12/31/2020. Baseline demographics, clinical characteristics, EGFR testing, and EGFRex20ins detection rates by sex, race, and smoking history were summarized.

Results (if a Case Study enter NA)

A total of 67,281 patients with NSCLC were identified. EGFR testing increased from 44% in 2011 to 77% in 2020. Of all patients, 44,926 (66.8%) were tested: 50.8% female; 3.3% Asian; 16.0% never-smokers. Of all patients, 22,355 (33.2%) were not tested: 41.4% female; 1.2% Asian; 7.5% never-smokers. Of those tested, 6,245 (13.9%) patients had EGFR mutations: 65.9% female; 11.8% Asian; 48.4% never-smokers.

EGFRex20ins detection rates changed from 0.6% in 2011 to 1.0% in 2019 and 0.7% in 2020. Of those tested, 304 patients had EGFRex20ins: 58.2% female; 8.2% Asian; 50.3% never-smokers. EGFR testing was higher in females (71.2%) than males (62.8%), never-smokers (84.5%) than those with a smoking history (64.6%), and Asian patients (84.2%) than White (66.6%), Black (65.4%), or other patients (69.5%). Of those tested, EGFRex20ins mutations were detected in 0.8% of females (males: 0.6%), 2.2% of never-smokers (with smoking history: 0.4%), and 1.7% of Asians (White: 0.6%, Black: 0.6%, other patients: 0.7%) had EGFRex20ins. A similar trend was observed for EGFR mutations with higher proportions of females, never-smokers, and Asian patients affected.

Conclusion

EGFR testing and EGFRex20ins detection rates have increased. However, not all patient subgroups were tested at the same rate and undertesting occurred in all subgroups. Further education of specialists diagnosing NSCLC is warranted to ensure all patients receive biomarker testing and benefit from emerging EGFRex20ins- targeted therapies.

[Establishment of a prognostic Nomogram model for predicting the first 72-hour mortality in polytrauma patients]

OBJECTIVE

To establish a prognostic Nomogram model for predicting the risk of early death in polytrauma patients.

METHODS

Data extracted from a polytrauma study on Dryad, an open access database, was selected for secondary analysis. Patients from 18 to 65 years old with polytrauma in the original data were included. All patients with missing variables, such as blood lactic acid (Lac), Glasgow coma score (GCS) and injury severity score (ISS) at admission, were excluded. The differences of gender, age, Lac, ISS and GCS scores between the patients who died within 72 hours and those who survived were analyzed. The risk factors for 72-hour death were analyzed by Logistic regression, and the Nomogram prediction model was established using R software. The receiver operating characteristic (ROC) curve was used to evaluate the predictive ability of the model, and the Bootstrap method was used for internal verification by repeating sample for 1 000 times. Decision curve (DCA) was applied to analyze the clinical practical value of the model.

RESULTS

A total of 2 315 polytrauma patients were included. Logistic regression analysis showed that Lac, GCS score and age > 55 years old were the risk factors for early death in polytrauma patients [Lac: odds ratio (OR) = 1.36, 95% confidence interval (95%CI) was 1.29-1.42, P < 0.001; GCS score: OR = 0.76, 95%CI was 0.73-0.79, P < 0.001; age > 55 years old: OR = 1.92, 95%CI was 1.37-2.66, P < 0.001]. The prediction model was established by using the above risk factors and displayed by Nomogram. ROC curve analysis showed that the area under the ROC curve (AUC) of Nomogram model to predict the risk of death within 72 hours was 0.858, and the predictive ability of Nomogram model was significantly higher than that of Lac (AUC = 0.743), GCS score (AUC = 0.774) and ISS score (AUC = 0.699), all P < 0.05. The model calibration chart showed that the predicting probability was consistent with the actual occurrence probability, and the DCA showed that Nomogram model presented excellent clinical value in predicting the 72-hour death risk for polytrauma patients.

CONCLUSIONS

The prognostic Nomogram model presents significantly predictive value for the risk of death within 72 hours in polytrauma patients. Prognostic Nomogram model could offer individualized, visualized and graphical prediction pattern, and provide physicians with practical diagnostic tool for triage system and management of polytrauma according to precision medicine.

MACC1 silencing inhibits cell proliferation and induces cell apoptosis of lung adenocarcinoma cells through the β-catenin pathway

It has been documented that over-expression of metastasis-associated in colon cancer-1 (MACC1) is related to poor prognosis in non-small cell lung cancer (NSCLC). This study investigates the function and underlying molecular mechanisms of MACC1 in lung adenocarcinoma. Here, we firstly employed immunohistochemistry, western blotting, real-time PCR, and online database to demonstrate that MACC1 expression was elevated in tumor tissues compared with tumoradjacent or normal tissues. Real-time PCR, CCK-8, colony formation western blotting, Hoechst staining, and flow cytometry assays then evaluated the effects of MACC1 knockdown on the cell cycle, cell proliferation and apoptosis in A549  and H1299 adenocarcinoma cells. Result highlighted that MACC1 knockdown inhibited cell proliferation, induced G0/ G1 phase arrest and promoted cell apoptosis in vitro. Mechanistic analysis revealed it also up-regulated expression levels of bax, cleaved-caspase-3 and cleaved-PARP while down-regulating cyclin D1, c-myc, bcl-2, and β-catenin expression in A549 cells. Intriguingly, up-regulation of β-catenin suppressed G0/G1 phase arrest and apoptosis in MACC1-silenced A549 cells and this was accompanied by increased levels of cyclin D1, c-myc, and bcl-2. Collectively, our results indicate that MACC1 knockdown effectively inhibited cell proliferation and promoted apoptosis of lung adenocarcinoma cells by regulating the β-catenin pathway.

Low Wall Shear Stress Is Associated with Local Aneurysm Wall Enhancement on High-Resolution MR Vessel Wall Imaging

BACKGROUND AND PURPOSE

Some retrospective studies have found that the aneurysm wall enhancement on high-resolution MR vessel wall postgadolinium T1WI has the potential to distinguish unstable aneurysms. This study aimed to identify hemodynamic characteristics that differ between the enhanced and nonenhanced areas of the aneurysm wall on high-resolution MR vessel wall postgadolinium T1WI.

MATERIALS AND METHODS

TOF-MRA and high-resolution MR vessel wall T1WI of 25 patients were fused to localize the enhanced area of the aneurysm wall. Using computational fluid dynamics, we studied the aneurysm models. Mean static pressure, mean wall shear stress, and oscillatory shear index were compared between the enhanced and nonenhanced areas.

RESULTS

The aneurysmal enhanced area had lower wall shear stress (P < .05) and a lower oscillatory shear index (P = .021) than the nonenhanced area. In addition, the whole aneurysm had lower wall shear stress (P < .05) and a higher oscillatory shear index (P = .007) than the parent artery.

CONCLUSIONS

This study suggests that there are hemodynamic differences between the enhanced and nonenhanced areas of the aneurysm wall on high-resolution MR vessel wall postgadolinium T1WI.

Bioinformatics analysis of gene expression profiles in the rat cerebral cortex following traumatic brain injury

BACKGROUND

Traumatic brain injury (TBI) is a serious neurodisorder commonly caused by sports related events or violence. It is the leading cause of disability in people under 40.

AIM

In order to elucidate the molecular mechanism of the secondary injury after TBI.

MATERIALS AND METHODS

In this study, we downloaded gene expression profile on TBI model with sham controls for gene set enrichment analysis and pathway analysis.

RESULTS

At a q-value of 5%, 361 genes were up-regulated and 373 were down-regulated in samples obtained at 48 hours after TBI. Functional analyses revealed that steroid biosynthesis, cell cycle, metal ion transport, inflammation and apoptosis were significantly dysregulated during the late period after trauma. In addition, MAPK3 (mitogen-activated protein kinase 3), was identified as the hub node in the protein-protein interaction (PPI) network constructed by the differentially expressed genes (DEGs).

CONCLUSIONS

Further elucidation of genes and proteins in our study may reveal their potential as novel therapeutic targets.

Clinical activity observed in a phase I dose escalation trial of an oral c-met and ALK inhibitor, PF-02341066

3509

Background: PF-02341066 (PF) is a selective, ATP-competitive, small molecule oral inhibitor of the c-Met/HGFR and ALK receptor tyrosine kinases that has not previously been tested in humans. A Phase 1 dose-escalation trial evaluating PF as an oral single agent was conducted to investigate safety, PK and PD in patients (pts) with advanced cancer (excluding leukemias). Methods: PF was administered under fasting conditions QD or BID on a continuous schedule to pts in successive dose-escalating cohorts at doses ranging from 50 mg QD to 300 mg BID. Pts with advanced cancer were enrolled in the study. Results: Thirty-seven pts were enrolled into the dose escalation part of the study. Tumor types included colorectal, pancreatic, sarcoma, ALCL and NSCLC. The MTD was 250 mg BID. Three DLTs were observed: grade 3 increase in ALT (1 pt at 200 mg QD) and grade 3 fatigue (2 pts at 300 mg BID). The most common AEs were nausea, emesis, fatigue and diarrhea. Nausea and emesis were independent of dose or duration of treatment. Mean AUC (30–57% CV) and Cmax (36–69% CV) increased proportionally with dose from 100 mg QD to 300 mg BID. The median terminal half-life was 46 hours. A 2- to 4-fold increase in the oral midazolam (MDZ) AUC was observed following 28-days of PF dosing at 100 mg QD (n = 3) and 300 mg BID (n = 2), respectively, suggesting PF to be an inhibitor of CYP3A. Ten pts have entered an enriched RP2D cohort of pts with tumors harboring c-Met amplification/gene mutation or ALK fusion genes. There has been 1 confirmed PR in a sarcoma pt with ALK rearrangement (inflammatory myofibroblastic tumor). Among 10 NSCLC pts whose tumors harbor EML4-ALK rearrangement, 1 pt has had a PR, 2 pts have achieved unconfirmed PR and 4 pts have had SD (3 have experienced reduction in tumor burden by ∼20% in measurable lesions and 1 has been treated for 28 weeks). Conclusions: The MTD of PF is 250 mg BID. The major AEs were fatigue or GI-related, and all AEs were manageable and reversible. There was no evidence of non-linear PK at PF doses >100 QD. Treatment with PF-02341066 resulted in promising clinical activity against tumors carrying activating ALK gene rearrangements. Further study of PF in pts with ALK-dependent tumors is warranted.

[Table: see text]

Proposed staging system modifications for advanced bronchioloalveolar carcinoma supported with a population-based validation study

7559

Background: Concordant with surgical series, our prior analysis of US SEER data demonstrates improved survival for BAC patients with stage IIIB disease due to multiple lesions in the same lobe compared to other stage IIIB patients, and also for patients with ipsilateral multicentric BAC compared to those with distant metastasis. In order for the BAC staging system to accurately reflect survival for these distinct patient subsets, we propose a revised staging system for advanced BAC and validate this system using California Cancer Registry (CCR) data. Methods: A case-only analysis of incident BAC cases in CCR during 1999–2003 was conducted. Based on modeling from our prior SEER analysis, the T4 descriptor for multiple tumors in the same lobe was downstaged to T3, and the M1 descriptor for ipsilateral multicentric BAC was downstaged to T4. The primary outcome measured was overall survival (OS). OS univariate analyses were conducted using the Kaplan-Meier method; multivariate survival analyses were performed using Cox proportional hazards ratios. Results: 1909 incident cases of histologically-confirmed BAC were analyzed. Using the proposed criteria, 162 (25%) of the 654 advanced BAC cases were reclassified: 73 cases with multiple lesions in the same lobe as T3 (stage II T3N0M0 [n=53] or T3NXM0 [n=1], stage IIIA T3N1–2M0 [n=18], stage IIIB T3N3M0 [n=1]); 89 cases with ipsilateral intrapulmonary metastasis were reclassified as T4 (stage IIIB, T4N1- 3M0). Univariate OS analysis of this validation set reveals an improved fit for the proposed staging system compared to the existing staging system ( Table 1 ). Analysis by stage reveals improvement in this proposed prognostic model over the existing staging system on multivariate survival analysis after adjustment for relevant clinicopathologic variables ( Table ). Conclusions: Our proposed BAC staging system modifications more accurately reflect survival characteristics for this unique type of non-small-cell lung cancer.

[Table: see text]

A novel intermediate endpoint for predicting overall survival in men with metastatic castration-recurrent prostate cancer (CRPC)

5113

Background: In this proposed study, we developed and validated a novel composite clinical benefit endpoint constructed from symptoms that have intrinsic clinical importance in 800 men with CRPC who were treated with front-line chemotherapy. Methods: Data from nine multimember trials (five phase II and four randomized phase III studies) conducted by the Cancer and Leukemia Group B (CALGB) from 1992–2004 were combined. Eligible patients had progressive adenocarcinoma of the prostate during androgen ablation (despite castrate testosterone levels), an ECOG performance status of 0–2, adequate hematologic, renal and hepatic functions. The tripartite composite clinical benefit endpoint (TCCBE) had three components: one based on disease progression (whether it be PSA, bone, or soft tissue progression), and the second based on weight loss (defined as at least 10% decline from baseline) or on performance status (PS) decline (by at least one level) to capture clinical deterioration. The third component was based on pain control and opioid analgesic use (no or yes). For a person to fall in the TCCBE “yes” category, at least two of the three components had to be recorded as no. For instance, if a patient at 3 months had no progression, no change in weight and did not use opioid analgesic, then he will be classified in the “yes” group and for the purpose of this analysis was considered as someone who achieved “clinical benefit”. The sample was randomly split into 526 (67%) and 274 (33%) men in the training and testing datasets, respectively. Results: From the training dataset, the median survival times in men who had and did not have clinical benefit were 20.9 months (95% confidence interval (CI) = 18.5–22.8) and 11.1 months (95% = 8.79–12.6, p- value<0.001). In the testing dataset, the median survival times in men with and without clinical benefit were 21.7 months (95% CI= 19.1–26.1) and 8.8 months (95% CI= 7.8–11.6) and in men. The hazard ratio (HR) for men with a clinical benefit compared to men without was 0.52 (95% CI= 0.43–0.62, P<0.001). Conclusions: The TCCBE is a statistically significant intermediate endpoint for predicting overall survival. Prospective validation of this endpoint is needed.

No significant financial relationships to disclose.

An elevated body mass (BMI) index predicts for better clinical outcomes in men with metastatic hormone refractory prostate cancer (HRPC)

4556

Background: Previous articles have reported that an elevated BMI was associated with an increased risk of biochemical failure in hormone sensitive patients. We asked the question as to whether an elevated BMI predicts for worst clinical outcomes, namely overall survival (OS) and prostate-cancer survival (PCS), among 1,216 men with HRPC. Methods: Patients were enrolled on eight clinical trials conducted by the Cancer and Leukemia Group B (CALGB). Eligible patients had progressive prostate cancer during androgen deprivation therapy (with documented castrate levels of testosterone), an ECOG performance status of 0–2, adequate hematologic, renal and hepatic function. We used the NIH definition to classify patients as: normal (<25 kg/m2), overweight (25–29 kg/m2 ), mildly obese (30–34 kg/m2), and moderately to severely obese (≥35 kg/m2). PCS was defined as the time from study entry to the time of death due to prostate cancer. The proportional hazards model was used to explore the prognostic significance of BMI in predicting OS and PCS. Results: The median BMI was 27.7 kg/m2 (inter-quartile range = 25.2–31.0 kg/m2 ). Twenty three percent (285/1216) of the patients had normal BMI, 46% (555/1216) were overweight, 23% (280/1216) were mildly obese, and 8% (96/1216) were moderately to severely obese. In multivariate analysis, adjusting for age, race, performance status, hemoglobin, PSA, LDH, alkaline phosphatase, testosterone, years since diagnosis, presence of visceral disease and Gleason scores, BMI was a statistically significant predictor of OS and PCS. Compared to normal men, the hazard ratios (HR) of overweight patients was 0.80 (95% CI = 0.69–0.93, p-value = 0.003), for mildly obese patients was 0.86 (95% CI = 0.72–1.02, p-value = 0.087) and for moderately to severely obese men it was 0.60 (95% CI = 0.47–0.78, p-value < 0.001). In addition, the HRs for PCS for overweight patients was 0.83 (95% CI = 0.70–0.97, p-value = 0.023), was 0.88 (95% CI = 0.72–1.06, p-value = 0.179) for mildly obese and for moderately to severely obese was 0.62 (95% CI = 0.47–0.81, p-value = 0.001) compared to men with normal BMI. Conclusions: Contrary to what was reported, these findings demonstrate an inverse relationship between BMI and clinical outcomes in men with HRPC.

[Table: see text]

Production of a novel FK520 analog in Streptomyces hygroscopicus: improving titer while minimizing impurities

FK520, also called ascomycin, is an immunosuppressive agent produced by Streptomyces hygroscopicus. Engineering the polyketide synthase genes of the parent strain generated novel FK520 analogs with the potential for improved in vivo stability. By replacing the acyl transferase (AT) domain in the polyketide synthase module 8 with an AT specific for methylmalonyl CoA (the rapamycin AT 3), the strain produced 13-desmethoxy-13-methyl-FK520 (13dmmFK520). Process development and scale-up studies of this recombinant S. hygroscopicus strain producing 13dmmFK520 are described here. Production kinetics and compound stability in fermentation broth were significantly different compared to the native FK520. Fermentation of the new strain resulted in the synthesis of a contaminating substance that co-purified with the 13dmmFK520. To optimize 13dmmFK520 production and to facilitate purification, growth parameters and media development were examined. Although a medium was identified that increased product titers by ca. 300%, the ratio of impurity to product was doubled. Lower dissolved oxygen (20% compared to 50% and 80%) increased titers by 20% with no appreciable effect on the concentration of impurity. Increasing the fermentation pH from 6.0 to 6.5 did not change the 13dmmFK520 titer, but reduced the impurity-to-product ratio by approximately 450%.

Modulation of epothilone analog production through media design

Recently, the epothilone polyketide synthase (PKS) was successfully introduced into a heterologous production host for the large-scale production of epothilone D. We have found that at least three other epothilones can also be produced as the major fermentation product of this recombinant strain by supplementation of specific substrates to the production media. Addition of acetate or propionate to the media results in modulation of the epothilone D:C ratio, whereas addition of L-serine with either acetate or propionate yields epothilone H(1) or H(2) as the major product. This strategy permits production of at least four novel epothilones by culturing a single host with a genetically modified epothilone PKS in various media.

New anti-huntingtin monoclonal antibodies: implications for huntingtin conformation and its binding proteins

We produced eight anti-huntingtin (Htt) monoclonal antibodies (mAbs), several of which have novel binding patterns. Peptide array epitope mapping shows that mAbs MW1-6 specifically bind the polyQ domain of Htt exon 1. On Western blots of extracts from mutant Htt knock-in mouse brain and Huntington's disease lymphoblastoma cell lines, MW1-5 all strongly prefer to bind to the expanded polyQ repeat form of Htt, displaying no detectable binding to normal Htt. These results suggest that the polyQ domain can assume different conformations that are distinguishable by mAbs. This idea is supported by immunohistochemistry with wild type (WT) and mutant Htt transgenic mouse (R6) brains. Despite sharing the same epitope and binding preferences on Western blots, MW1-5 display distinct staining patterns. MW1 shows punctate cytoplasmic and neuropil staining, while MW2-5 strongly stain the neuronal Golgi complex. MW6, in contrast, stains neuronal somas and neuropil. In addition, despite their preference for mutant Htt on blots, none of these mAbs show enhanced staining of R6 brains over WT, and show no binding of the Htt-containing nuclear inclusions in R6 brains. This suggests that in its various subcellular locations, the polyQ domain of Htt either takes on different conformations and/or is differentially occluded by Htt binding proteins. In contrast to MW1-6, MW7, and 8 can differentiate transgenic from WT mice by staining nuclear inclusions in R6/2 brain; MW8 displays no detectable staining in WT brain and stains only inclusions in R6/2 brain. Epitope mapping reveals that MW7 and 8 specifically bind the polyP domains and amino acids 83-90, respectively. As with MW1-6, the epitopes for MW7 and 8 are differentially available in the various subcellular compartments where Htt is found.

Enhancing the atom economy of polyketide biosynthetic processes through metabolic engineering

Polyketides, a large family of bioactive natural products, are synthesized from building blocks derived from alpha-carboxylated Coenzyme A thioesters such as malonyl-CoA and (2S)-methylmalonyl-CoA. The productivity of polyketide fermentation processes in natural and heterologous hosts is frequently limited by the availability of these precursors in vivo. We describe a metabolic engineering strategy to enhance both the yield and volumetric productivity of polyketide biosynthesis. The genes matB and matC from Rhizobium trifolii encode a malonyl-CoA synthetase and a putative dicarboxylate transport protein, respectively. These proteins can directly convert exogenous malonate and methylmalonate into their corresponding CoA thioesters with an ATP requirement of 2 mol per mol of acyl-CoA produced. Heterologous expression of matBC in a recombinant strain of Streptomyces coelicolor that produces the macrolactone 6-deoxyerythronolide B results in a 300% enhancement of macrolactone titers. The unusual efficiency of the bioconversion is illustrated by the fact that approximately one-third of the methylmalonate units added to the fermentation medium are converted into macrolactones. The direct conversion of inexpensive feedstocks such as malonate and methylmalonate into polyketides represents the most carbon- and energy-efficient route to these high value natural products and has implications for cost-effective fermentation of numerous commercial and development-stage small molecules.

In vitro study of possible role of dietary fiber in lowering postprandial serum glucose

There have been many reports concerning the role of dietary fiber in lowering postprandial serum glucose, and the main mechanism was regarded as the viscosity of different dietary fibers in hampering diffusion of glucose and postponing absorption and digestion of carbohydrates. In this paper, two kinds of water-insoluble dietary fibers, water-insoluble dietary fiber of wheat bran and enzyme-resistant starch of maize amylose, and four kinds of water-soluble dietary fibers, water-soluble dietary fiber of wheat bran, carboxymethyl cellulose, guar gum, and xanthan gum, were used to investigate their postprandial serum glucose lowering mechanism in vitro. The results showed that these dietary fibers lowered postprandial serum glucose levels at least by three mechanisms. First, dietary fibers increase the viscosity of small intestine juice and hinder diffusion of glucose; second, they bind glucose and decrease the concentration of available glucose in the small intestine; and, third, they retard alpha-amylase action through capsuling starch and the enzyme and might directly inhibit the enzyme. All of these decreased the absorption rate of glucose and the concentration of postprandial serum glucose.

A geminivirus replication protein interacts with the retinoblastoma protein through a novel domain to determine symptoms and tissue specificity of infection in plants

Geminiviruses replicate in nuclei of mature plant cells after inducing the accumulation of host DNA replication machinery. Earlier studies showed that the viral replication factor, AL1, is sufficient for host induction and interacts with the cell cycle regulator, retinoblastoma (pRb). Unlike other DNA virus proteins, AL1 does not contain the pRb binding consensus, LXCXE, and interacts with plant pRb homo logues (pRBR) through a novel amino acid sequence. We mapped the pRBR binding domain of AL1 between amino acids 101 and 180 and identified two mutants that are differentially impacted for AL1-pRBR interactions. Plants infected with the E-N140 mutant, which is wild-type for pRBR binding, developed wild-type symptoms and accumulated viral DNA and AL1 protein in epidermal, mesophyll and vascular cells of mature leaves. Plants inoculated with the KEE146 mutant, which retains 16% pRBR binding activity, only developed chlorosis along the veins, and viral DNA, AL1 protein and the host DNA synthesis factor, proliferating cell nuclear antigen, were localized to vascular tissue. These results established the importance of AL1-pRBR interactions during geminivirus infection of plants.

Precursor-directed biosynthesis of 6-deoxyerythronolide B analogs in Streptomyces coelicolor: understanding precursor effects

A fermentation process employing precursor-directed biosynthesis is being developed for the manufacture of 6-deoxyerythronolide B (6-dEB) analogues. Through a plasmid-based system in Streptomyces coelicolor, 6-dEB synthesis is catalyzed by 6-dEB synthase (DEBS). 6-dEB synthesis is abolished by inactivation of the ketosynthase (KS) 1 domain of DEBS but can be restored by providing synthetic activated diketides. Because of its inherent catalytic flexibility, the KS1-deficient DEBS is capable of utilizing unnatural diketides to form various 13-substituted 6-dEBs. Here we characterize process variables associated with diketide feeding in shake-flask experiments. 13-R-6-dEB production was found to depend strongly on diketide feed concentrations, on the growth phase of cultures at feeding time, and on the R-group present in the diketide moiety. In all cases a major portion of the fed diketides was degraded by the cells.