Growth couples temporal and spatial fluctuations of tissue properties during morphogenesis

Living tissues display fluctuations - random spatial and temporal variations of tissue properties around their reference values - at multiple scales. It is believed that such fluctuations may enable tissues to sense their state or their size. Recent theoretical studies developed specific models of fluctuations in growing tissues and predicted that fluctuations of growth show long-range correlations. Here we elaborated upon these predictions and we tested them using experimental data. We first introduced a minimal model for the fluctuations of any quantity that has some level of temporal persistence or memory, such as concentration of a molecule, local growth rate, or mechanical property. We found that long-range correlations are generic, applying to any such quantity, and that growth couples temporal and spatial fluctuations, through a mechanism that we call 'fluctuation stretching' - growth enlarges the lengthscale of variation of this quantity. We then analysed growth data from sepals of the model plant Arabidopsis and we quantified spatial and temporal fluctuations of cell growth using the previously developed Cellular Fourier Transform. Growth appears to have long-range correlations. We compared different genotypes and growth conditions: mutants with lower or higher response to mechanical stress have lower temporal correlations and longer-range spatial correlations than wild-type plants. Finally, we used theoretical predictions to merge experimental data from all conditions and developmental stages into an unifying curve, validating the notion that temporal and spatial fluctuations are coupled by growth. Altogether, our work reveals kinematic constraints on spatiotemporal fluctuations that have an impact on the robustness of morphogenesis.

Robust organ size in Arabidopsis is primarily governed by cell growth rather than cell division patterns

Organ sizes and shapes are highly reproducible, or robust, within a species and individuals. Arabidopsis thaliana sepals, which are the leaf-like organs that enclose flower buds, have consistent size and shape, which indicates robust development. Counterintuitively, variability in cell growth rate over time and between cells facilitates robust development because cumulative cell growth averages to a uniform rate. Here we investigate how sepal morphogenesis is robust to changes in cell division but not robust to changes in cell growth variability. We live image and quantitatively compare the development of sepals with increased or decreased cell division rate ( lgo mutant and LGO overexpression, respectively), a mutant with altered cell growth variability ( ftsh4 ), and double mutants combining these. We find that robustness is preserved when cell division rate changes because there is no change in the spatial pattern of growth. Meanwhile when robustness is lost in ftsh4 mutants, cell growth accumulates unevenly, and cells have disorganized growth directions. Thus, we demonstrate in vivo that both cell growth rate and direction average in robust development, preserving robustness despite changes in cell division.

Summary statement

Robust sepal development is preserved despite changes in cell division rate and is characterized by spatiotemporal averaging of heterogeneity in cell growth rate and direction.

[Enhance the management of cardiac arrest and improve the prognosis of the patients]

Cardiac arrest is one of the major public health problems with sudden onset, high mortality and high disability rate. The prevalence of cardiovascular disease continues to rise and the burden of cardiac arrest is increasing in China. It is of great significance to explore more effective prevention and treatment measures to improve the prognosis of patients with cardiac arrest. This article discusses the relevant progress on the treatment ability of emergency and critical cardiovascular diseases, medicines and technologies for cardiac arrest care, and registry studies of cardiac arrest, to further promote the effective improvement of key capacities at various stages of the prevention and treatment of cardiac arrest in China.

[Clinical efficacy of the treatment of bilateral gluteal muscle contracture by inside-out iliotibial band release under arthroscopy in the supine position]

Objective: To investigate the clinical efficacy of bilateral gluteal muscle contracture treated with inside-out iliotibial band release under arthroscopy in the supine position. Methods: A prospective non-randomized controlled trial. Forty-six patients admitted to the Department of Sports Medicine, Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital from April 2021 to August 2022 for bilateral gluteal muscle contracture and proposed surgical treatment were enrolled. The subjects were divided into two groups according to the preferred surgical protocols of the patients: the supine position group was treated with inside-out iliotibial band release under arthroscopy in the supine position, and the operation in lateral position group was carried out with outside-in iliotibial band release under arthroscopy in the lateral position. The total duration of non-surgical operations and the total duration of surgical operations were recorded for all patients. The gluteal muscle contracture disability scale within 3 days before surgery and at least 2 months after surgery were compared between the two groups, and the occurrence of complications between the two groups was compared too. Results: There were 26 cases in the supine position group, 11 males and 15 females with a mean age of (31.8±7.3) years; and there were 20 cases in the lateral position group, 7 males and 13 females with a mean age of (30.6±6.3) years. The differences in gender, age, body mass index (BMI) and postoperative follow-up time between the two groups were not statistically significant (all P>0.05). The total duration of non-surgical operations was shorter in the supine position group than in the lateral position group [(47.9±10.4) min vs (63.9±7.5) min, P<0.001]. There was no statistically significant difference in the total duration of surgical operations between the supine position group and the lateral position group [31.0(27.0, 43.5) min vs 33.0(24.8, 38.0) min, P>0.05]. The postoperative gluteal muscle contracture disability scales were significantly improved in both the supine position and lateral position groups when compared with those before the operation [93.0 (85.0, 98.0) vs 61.0 (50.5, 66.8), P<0.001 and 88.5±6.9 vs 63.6±9.6, P<0.001, respectively]. There was no statistically significant difference in the gluteal muscle contracture disability scale between the supine position and lateral position groups before and 2 months after surgery [59.3±11.9 vs 63.6±9.6 and 93.0 (85.0, 98.0) vs 89.5(84.0, 94.8), both P>0.05, respectively]. Two patients in each group developed subcutaneous hematoma after surgery, and all of them resolved within 2 weeks after surgery, the difference in complication incidence rate was not statistically significant (P>0.05). No postoperative complications such as fat liquefaction in the operated area, infection, decreased hip abductor muscle strength or nerve injury in the lower extremity were observed in both groups. Conclusion: The treatment of bilateral gluteal muscle contracture by inside-out iliotibial band release under arthroscopy in the supine position can effectively improve clinical efficiency, with definite efficacy, and it is an operative program worth promoting.

[Predictive value of ultrasound-guided anesthesia injection in arthroscopy for borderline developmental dysplasia of the hip]

Objective: To evaluate the value of ultrasound-guided intra-articular anesthetic injection in predicting postoperative outcomes for borderline developmental hip dysplasia (BDDH). Methods: A follow-up study. The clinical data of 37 BDDH patients who received ultrasound-guided intra-articular anesthetic injection and arthroscopic examination in the Department of Sports Medicine, Senior Department of Orthopedics, the Fourth Medical Center of PLA General Hospital from May 2018 to February 2021 were retrospectively analyzed. Among them, there were 17 males and 20 females with a mean age of (37.9±12.8) years. All patients underwent ultrasound-guided intra-articular anesthetic injection prior to arthroscopy, and were evaluated with hip physical examination before and after injection, as well as before and after arthroscopy, in order to obtain the visual analog score (VAS) of pain for seven assessments. The total VAS score was calculated based on these evaluations. Follow-up was conducted for at least 12 months. The effective rate of injection referred to the ratio of the improvement of VAS score after anesthetic injection to the total VAS score before injection. Pearson correlation analysis and Bland-Altman analysis were used to test the correlation between modified Harris hip score (mHHS) after ultrasound-guided intra-articular anesthetic injection and mHHS score after arthroscopic surgery. A binary logistic regression model was established to analyze the substantial clinical benefit (SCB) for patients. Following the logistic regression analysis, a receiver operating characteristic (ROC) curve was constructed to evaluate the predictive power of ultrasound-guided intra-articular anesthetic injection in achieving SCB in those patients. The optimal cut-off value for injection efficacy was determined based on the ROC curve when SCB was achieved. Results: The follow-up time for all patients was (26.3±7.6) months. After anesthetic injection for 20 minutes, the total VAS score of pain [M(Q₁,Q₃)] decreased from 13(8,23) points before injection to 1(0,4) points; and the mHHS score [M(Q₁,Q₃)] increased from 60(46,70) points before arthroscopy to 90(84,96) points after, with statistically significant differences before and after injection and before and after arthroscopy (both P<0.001). Pearson correlation analysis showed that the mHHS score after intra-articular anesthetic injection was positively correlated with the mHHS score after surgery (r=0.961, P<0.001). The area under the ROC curve for predicting SCB after arthroscopy with ultrasound-guided intra-articular anesthetic injection was 0.769 (95%CI: 0.561-0.976), the Youden index was 0.663, the cut-off value was 0.569 2, the sensitivity was 96.3%, and the specificity was 70.0%. Conclusions: The results of ultrasound-guided intra-articular anesthetic injection before arthroscopy can indicate the presence of intra-articular lesions, and the degree of pain relief after injection is proportional to the functional recovery after arthroscopy. Patients with intra-articular anesthetic injection efficacy>56.92% have better results in hip arthroscopy.

Rotary properties of hybrid F1-ATPases consisting of subunits from different species

F₁-ATPase (F₁) is an ATP-driven rotary motor protein ubiquitously found in many species as the catalytic portion of F_oF₁-ATP synthase. Despite the highly conserved amino acid sequence of the catalytic core subunits: α and β, F₁ shows diversity in the maximum catalytic turnover rate V_max and the number of rotary steps per turn. To study the design principle of F₁, we prepared eight hybrid F₁s composed of subunits from two of three genuine F₁s: thermophilic Bacillus PS3 (TF₁), bovine mitochondria (bMF₁), and Paracoccus denitrificans (PdF₁), differing in the V_max and the number of rotary steps. The V_max of the hybrids can be well fitted by a quadratic model highlighting the dominant roles of β and the couplings between α-β. Although there exist no simple rules on which subunit dominantly determines the number of steps, our findings show that the stepping behavior is characterized by the combination of all subunits.

[Outcomes of fluoroscopy-free hip arthroscopy technique in the treatment of femoroacetabular impingement syndrome]

Objective: To evaluate the effect of fluoroscopy-free technique in the arthroscopic treatment of femoroacetabular impingement syndrome (FAIS). Methods: A retrospective cohort study. Clinical data of FAI patients treated with hip arthroscopy in the No.4 Medical Center, PLA General Hospital from October 2018 to December 2021 were retrospectively analyzed. The patients were divided into two groups according to the surgical procedure: the fluoroscopy group and the fluoroscopy-free group. The operation time and modified Harris hip score (mHHS), international hip outcome tool (iHOT12) and visual analogue scale (VAS) of hip joint pain before and after the operation were observed and compared between the two groups. And the incidence of surgical complications in the two groups were compared too. Results: A total of 460 patients (213 males and 247 females) [aged (32.6±8.3) years (15-67 years)] with valid follow-up were included in this study. There were 275 cases in the fluoroscopy-free group and 185 cases in the fluoroscopy group. The operation time was shorter in the fluoroscopy-free group when compared with that in the fluoroscopy group, and the difference was statistically significant [(93.36±12.54) min vs (115.62±6.03) min, P<0.001]. In both groups, the VAS scores decreased and the mHHS scores and iHOT12 scores improved significantly at the last follow-up when compared with those before the operation (all P<0.001); however, there was no significant difference in the scores between the two groups (all P>0.05). The complication rate in the fluoroscopy-free group was 10.18% (28/275), and it was 10.81%(20/185) in the fluoroscopy group (P=0.829). Conclusion: Fluoroscopy-free hip arthroscopy technique for FAI can avoid radiation and shorten the operation time, but it does not increase the incidence of complications with reliable clinical outcomes.

Shape-aware stochastic neighbor embedding for robust data visualisations

Background

The t-distributed Stochastic Neighbor Embedding (t-SNE) algorithm has emerged as one of the leading methods for visualising high-dimensional (HD) data in a wide variety of fields, especially for revealing cluster structure in HD single-cell transcriptomics data. However, t-SNE often fails to correctly represent hierarchical relationships between clusters and creates spurious patterns in the embedding. In this work we generalised t-SNE using shape-aware graph distances to mitigate some of the limitations of the t-SNE. Although many methods have been recently proposed to circumvent the shortcomings of t-SNE, notably Uniform manifold approximation (UMAP) and Potential of heat diffusion for affinity-based transition embedding (PHATE), we see a clear advantage of the proposed graph-based method.

Results

The superior performance of the proposed method is first demonstrated on simulated data, where a significant improvement compared to t-SNE, UMAP and PHATE, based on quantitative validation indices, is observed when visualising imbalanced, nonlinear, continuous and hierarchically structured data. Thereafter the ability of the proposed method compared to the competing methods to create faithfully low-dimensional embeddings is shown on two real-world data sets, the single-cell transcriptomics data and the MNIST image data. In addition, the only hyper-parameter of the method can be automatically chosen in a data-driven way, which is consistently optimal across all test cases in this study.

Conclusions

In this work we show that the proposed shape-aware stochastic neighbor embedding method creates low-dimensional visualisations that robustly and accurately reveal key structures of high-dimensional data.

[Analytical performance verification protocols and performance specifications of platelet-dependent von Willebrand factor activity testing]

Objective: To investigate the analytical performance verification protocols and performance specifications of platelet-dependent von Willebrand factor (VWF) activity testing (VWF:GPIbM) for clinical laboratories. Methods: According to Clinical Laboratory Standards Institute (CLSI) documents and National Health Standard of China, the performance verification of VWF:GPIbM was designed and implemented using Sysmex CS-5100 instrument and its corresponding reagents. (1) Precision verification: Two commercial quality control samples (with normal and low activity levels) and three plasma pools (with activity range from 5.0% to 150.0%) were prepared. Each sample was tested five times daily for five consecutive days. The coefficient of variation (CV) of intra-and inter-run precisions were calculated, and the precision evaluation criterion was set according to package inserts. (2) Trueness verification: The calibrator was diluted to five reference materials with activity values of 5.2%, 31.2%, 62.4%, 104.0% and 138.7%, and each reference material was tested five times daily for five consecutive days. The bias between the measured value and the reference value was calculated, and the trueness evaluation criterion was set according to the total allowable error. (3) Linearity verification: Ten pooled plasmas with theoretical value range from 3.6% to 160.4% were prepared for the linearity verification of two calibration curves set by the manufacturer (i.e. low range and normal range calibration curve). Each pooled plasma was tested three times in a single run. The slope and R² of linear regression of mean of measured value and theoretical value, as well as bias, were calculated, and the linearity evaluation criterion was set according to National Health Standard of China and package inserts. (4) Limit of quantitation verification: The calibrator was diluted to two reference materials with activity values of 3.3% and 2.7%, and each material was tested twelve times. The limit of quantitation evaluation criterion was set according to CLSI document. Results: The CVs of intra-and inter-run were 1.0%-2.5% and 1.1%-2.6%, respectively. The biases of trueness verification were -0.4%, 1.0%, -2.6%, 0.3% and -2.7%, respectively. The linearity verification results of low range (3.6%-31.8%) and normal range (28.4%-160.4%) showed that the slopes of regression equation were 1.021 7 and 0.996 2, respectively, R² were 0.993 5 and 0.993 9, respectively, and the biases with 0-1.8% and -10.1%-0 of plasmas met the criterion. The biases ranged from -0.4% to 0.3% of test results in the verification of limit of quantitation met the criterion. Conclusion: The verification results of VWF:GPIbM assay for precision, trueness, linearity and limit of quantification meet the performance requirements indicated in the package inserts and the criteria set in this study, which can be taken as a reference of performance verification for the clinical laboratories.

Shepherd: Accurate Clustering for Correcting DNA Barcode Errors

Motivation

DNA barcodes are short, random nucleotide sequences introduced into cell populations to track the relative counts of hundreds of thousands of individual lineages over time. Lineage tracking is widely applied, e.g. to understand evolutionary dynamics in microbial populations and the progression of breast cancer in humans. Barcode sequences are unknown upon insertion and must be identified using next-generation sequencing technology, which is error prone. In this study, we frame the barcode error correction task as a clustering problem with the aim to identify true barcode sequences from noisy sequencing data. We present Shepherd, a novel clustering method that is based on an indexing system of barcode sequences using k-mers, and a Bayesian statistical test incorporating a substitution error rate to distinguish true from error sequences.

Results

When benchmarking with synthetic data, Shepherd provides barcode count estimates that are significantly more accurate than state-of-the-art methods, producing 10–150 times fewer spurious lineages. For empirical data, Shepherd produces results that are consistent with the improvements seen on synthetic data. These improvements enable higher resolution lineage tracking and more accurate estimates of biologically relevant quantities, e.g. the detection of small effect mutations.

Availability and implementation

A Python implementation of Shepherd is freely available at: https://www.github.com/Nik-Tavakolian/Shepherd.

Supplementary information

Supplementary data are available at Bioinformatics online.

[Current status of CD34+cell enumeration assay in clinical laboratories and its improvement]

Objective: To investigate the current status and problems of CD34⁺ cell enumeration in clinical laboratories and provide suggestions for the development of quality improvement programs. Methods: A total of 101 laboratories participating in the national external quality assessment program of CD34⁺cell enumeration were surveyed. Questionnaires and quality assessment materials were distributed to collect information on assay methodology and testing results. Quality control requirements for CD34⁺cell enumeration were determined according to the international guidelines, and the compliance of the surveyed laboratories was analyzed. Testing results were analyzed in groups and compared with the College of American Pathologists (CAP) quality assessment data. Results: A total of 97 laboratories returned the questionnaires and 99 laboratories returned the results of quality assessment materials. The questionnaire data showed high compliance rates of quality control requirements such as gating protocols, pipetting methods, and the number of cells acquired (92.8%, 83.9%, and 82.5% respectively). However, these laboratories had relatively low compliance rates such as the use of whole blood quality control materials for internal quality control, selection of erythrocyte lysing reagents, sample processing method, whether to report absolute count results, and quality control of equipment (5.2 %, 28.9%, 39.2%, 46.4%, and 55.7%, respectively). Testing results demonstrated that the coefficient of variation (CV) of percent counts was similar to the CAP quality assessment data, but the CV of absolute counts was greater than the CAP quality assessment data. Conclusions: Clinical laboratories have poor compliance with some quality control requirements and the variability of absolute count results between different laboratories is not satisfactory. Therefore, it is recommended that clinical laboratories should strengthen the training related to the quality control of CD34⁺cell enumeration, especially the absolute counting.

Robust organ size requires robust timing of initiation orchestrated by focused auxin and cytokinin signalling

Organ size and shape are precisely regulated to ensure proper function. The four sepals in each Arabidopsis thaliana flower must maintain the same size throughout their growth to continuously enclose and protect the developing bud. Here we show that DEVELOPMENT RELATED MYB-LIKE 1 (DRMY1) is required for both timing of organ initiation and proper growth, leading to robust sepal size in Arabidopsis. Within each drmy1 flower, the initiation of some sepals is variably delayed. Late-initiating sepals in drmy1 mutants remain smaller throughout development, resulting in variability in sepal size. DRMY1 focuses the spatiotemporal signalling patterns of the plant hormones auxin and cytokinin, which jointly control the timing of sepal initiation. Our findings demonstrate that timing of organ initiation, together with growth and maturation, contribute to robust organ size.

[Study on commutability evaluation of reference materials for fibrinogen]

Objective: To discuss the commutability evaluation method of reference materials for fibrinogen measurement and evaluate the commutability of the Third WHO International Standard Fibrinogen Plasma (WHO 09/264), SSC/ISTH Secondary Coagulation Standard (SSC LOT4) and homemade reference materials (RM01, RM02) in order to provide suggestions on how to determine the suitable method of commutability evaluation and reliable traceability standard. Methods: The comparability of fibrinogen among different measurement systems were evaluated and WHO 09/264 was used to calibrate each system to improve the comparability if the comparability among different systems couldn't be accepted. Forty clinical samples and the reference materials randomly interspersed among the clinical samples were measured on Stago STA-R Evolution, Sysmex CS 5100, IL ACL TOP 700 simultaneously. Measurement results were pairwise analyzed by Deming regression and difference in bias approach according to the Clinical and Laboratory Standards Institute (CLSI) EP14-A3 protocol and the recommendations of the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC) working group on commutability, respectively. Results: The comparability of fibrinogen measurement among common systems could not meet the criterion. WHO 09/264 could improve the agreement among different measurement systems. The prediction interval of Deming regression was affected by the comparability of measurement systems, resulting in unreliable results. The difference in bias approach was more suitable because its criterion was related to the medical requirements. WHO 09/264 was commutable between Stago and Sysmex, inconclusive between Stago and IL, Sysmex and IL (The calibration effectiveness of WHO 09/264 showed that it was commutable among the three measurement systems). SSC LOT4 was commutable between Stago and Sysmex, inconclusive between Stago and IL, Sysmex and IL. RM01 and RM02 were commutable between all systems pairs assessed by difference in bias approach. Conclusions: There are differences in the results of two commutability evaluation approaches. The difference in bias approach is recommended for commutability evaluation. WHO International Standard and homemade reference materials can be used as traceability standard for fibrinogen measurement.

[Analysis of internal quality control data of complete blood count from laboratories participating in national external quality assessment]

Objective: To investigate current status and problems of internal quality control (IQC) of complete blood count in China so as to perform IQC normally. Methods: The IQC data of complete blood count for five parameters were collected from laboratories participating in national external quality assessment during 2012-2017 (totally 12 times), including WBC, RBC, Hb, Hct and PLT. After confirmation of all data, data for the 12 times were analyzed as follows.The proportions of using different levels of quality control materials were calculated.The 25th, 50th, 75th, 90th percentiles CV of data collected for the 12 times were calculated respectively and the trends of CV were observed over time.The difference of CV among laboratories running three control levels was compared.The CV of each parameter in 2017 was compared with precision requirements based on biological variation, health standards and German Medical Association Directive; The proportions of laboratories using different control rules were calculated. Results: After invalid data was excluded from those IQC data of laboratories for the 12 times external quality assessment (up to 2 402, as low as 1 449) from 2012 to 2017, the residual data (up to 2 332, as low as 1 431, accounting for 96.0%-99.2%) was used for analysis. 61.9%-66.1%, 18.2%-23.6% and 14.3%-17.3% of laboratories ran one, two and three control levels respectively, and the proportions of laboratories running more than two control levels increased from 33.9% to 38.1%. The decrease trend of the 75th, 90th percentiles CV of WBC, RBC, Hb, Hct for three levels, PLT for normal level and the 90th percentiles CV of PLT low level had statistically significance over time (P<0.05); the decrease trend of the 75th percentiles CV of PLT low level and 75th, 90th percentiles CV of PLT high level had no statistically significance over time. The CV had significant difference between low and normal, low and high control level for WBC and PLT, while there were no difference between normal and high control levels. There were no significant difference of CV among three control levels for RBC, Hb, and Hct. Except for the CV of Hct low, normal level and PLT low level, 85% of laboratories for the other parameters could meet the minimum precision requirements based on biological variation; more than 85% laboratories met the requirements of health standards; except for the CV of PLT low level, more than 80% laboratories met the requirements of German Medical Association Directive. The proportion of laboratories using 1(3s)/2(2s) quality control rules increased from 59.2% to 76.0%. Conclusions: During the past 6 years, the CV for IQC has shown a decrease trend over time. However, the control level and quality control rules used by some laboratories do not meet management requirements. The CV of Hct and PLT in a few laboratories do not meet the minimum requirements of the health standards, and need to implement quality improvements fatherly.

Linear Elastic Fracture Mechanics Characterization of an Anisotropic Shale

The existence of bedding planes in natural shale formations makes the fracture characterization remarkably complicated. To achieve a further understanding of the anisotropic crack extension behaviors of shale using a linear elastic fracture mechanics approach, four groups of three-point bending tests on Longmaxi shale from southeast Chongqing were conducted in this study with different bedding plane inclination angles. The fracture propagation paths were observed using a scanning electron microscope. The results indicated that cracks initiated along the bedding plane when the bedding plane inclination angle (i.e., the angle between the loading direction and the normal direction of the bedding plane) was relatively large; in contrast, cracks penetrated into the matrix and induced higher fracture toughness in cases with lower bedding plane inclination angle. Brittle fractures occurred in the tested shale, and the fracture strength was strongly dependent on the bedding plane inclination angle. Meanwhile, the stress field around the crack tip was analyzed theoretically. The results indicated that the crack tip stress field of anisotropic shale is not only determined by the stress intensity factor but also related to the elastic constants and bedding plane inclination angle. Furthermore, a criterion for determining whether a crack extends along the bedding plane was developed by distinguishing the differences in the strengths of the shale bedding and the matrix.

Heterogeneity and Robustness in Plant Morphogenesis: From Cells to Organs

Development is remarkably reproducible, producing organs with the same size, shape, and function repeatedly from individual to individual. For example, every flower on the Antirrhinum stalk has the same snapping dragon mouth. This reproducibility has allowed taxonomists to classify plants and animals according to their morphology. Yet these reproducible organs are composed of highly variable cells. For example, neighboring cells grow at different rates in Arabidopsis leaves, sepals, and shoot apical meristems. This cellular variability occurs in normal, wild-type organisms, indicating that cellular heterogeneity (or diversity in a characteristic such as growth rate) is either actively maintained or, at a minimum, not entirely suppressed. In fact, cellular heterogeneity can contribute to producing invariant organs. Here, we focus on how plant organs are reproducibly created during development from these highly variable cells.

Why plants make puzzle cells, and how their shape emerges

The shape and function of plant cells are often highly interdependent. The puzzle-shaped cells that appear in the epidermis of many plants are a striking example of a complex cell shape, however their functional benefit has remained elusive. We propose that these intricate forms provide an effective strategy to reduce mechanical stress in the cell wall of the epidermis. When tissue-level growth is isotropic, we hypothesize that lobes emerge at the cellular level to prevent formation of large isodiametric cells that would bulge under the stress produced by turgor pressure. Data from various plant organs and species support the relationship between lobes and growth isotropy, which we test with mutants where growth direction is perturbed. Using simulation models we show that a mechanism actively regulating cellular stress plausibly reproduces the development of epidermal cell shape. Together, our results suggest that mechanical stress is a key driver of cell-shape morphogenesis.

Effects of non-equilibrium angle fluctuation on F1-ATPase kinetics induced by temperature increase

F₁-ATPase (F₁) is an efficient rotary protein motor, whose reactivity is modulated by the rotary angle to utilize thermal fluctuation. In order to elucidate how its kinetics are affected by the change in the fluctuation, we have extended the reaction-diffusion formalism [R. Watanabe et al., Biophys. J., 2013, 105, 2385] applicable to a wider range of temperatures based on experimental data analysis of F₁ derived from thermophilic Bacillus under high ATP concentration conditions. Our simulation shows that the rotary angle distribution manifests a stronger non-equilibrium feature as the temperature increases, because ATP hydrolysis and P_i release are more accelerated compared with the timescale of rotary angle relaxation. This effect causes the rate coefficient obtained from dwell time fitting to deviate from the Arrhenius relation in P_i release, which has been assumed in the previous activation thermodynamic quantities estimation using linear Arrhenius fitting. Larger negative correlation is also found between hydrolysis and P_i release waiting time in a catalytic dwell with the increase in temperature. This loss of independence between the two successive reactions at the catalytic dwell sheds doubt on the conventional dwell time fitting to obtain rate coefficients with a double exponential function at temperatures higher than 65 °C, which is close to the physiological temperature of the thermophilic Bacillus.

Clones of cells switch from reduction to enhancement of size variability in Arabidopsis sepals

Organs form with remarkably consistent sizes and shapes during development, whereas a high variability in growth is observed at the cell level. Given this contrast, it is unclear how such consistency in organ scale can emerge from cellular behavior. Here, we examine an intermediate scale, the growth of clones of cells in Arabidopsis sepals. Each clone consists of the progeny of a single progenitor cell. At early stages, we find that clones derived from a small progenitor cell grow faster than those derived from a large progenitor cell. This results in a reduction in clone size variability, a phenomenon we refer to as size uniformization. By contrast, at later stages of clone growth, clones change their growth pattern to enhance size variability, when clones derived from larger progenitor cells grow faster than those derived from smaller progenitor cells. Finally, we find that, at early stages, fast growing clones exhibit greater cell growth heterogeneity. Thus, cellular variability in growth might contribute to a decrease in the variability of clones throughout the sepal.

Summary: Growth analyses of Arabidopsis sepals identify a tipping point in organ development, at which clones of cells change their growth pattern from size uniformization to size variability enhancement.

Extracting Subcellular Fibrillar Alignment with Error Estimation: Application to Microtubules

The order and orientation of cortical microtubule (CMT) arrays and their dynamics play an essential role in plant morphogenesis. To extract detailed CMT alignment structures in an objective, local, and accurate way, we propose an error-based extraction method that applies to general fluorescence intensity data on three-dimensional cell surfaces. Building on previous techniques to quantify alignments, our method can determine the statistical error for specific local regions, or the minimal scales of local regions for a desired accuracy goal. After validating our method with synthetic images with known alignments, we demonstrate the ability of our method to quantify subcellular CMT alignments on images with microtubules marked with green fluorescent protein in various cell types. Our method could also be applied to detect alignment structures in other fibrillar elements, such as actin filaments, cellulose, and collagen.

[Study and analysis of national current status and problems of anticoagulant proteins assay]

Objective: To investigate current status and problems of anticoagulant proteins assay in domestic laboratories so as to provide suggestions for implementing the standardization and quality improvement. Methods: Two hundred and seventy-four laboratories those had developed or prepared to do anticoagulant proteins assay were selected from one thousand and five hundred participants in the national coagulation screening External Quality Assessment(EQA) program by an internet survey and then a questionnaire and quality control materials were sent to them to carry out a further survey. The questionnaire information was analyzed statistically. The results of quality control materials were grouped by the reagents and the average, median, standard deviation(s), coefficient variation(CV) of each group were calculated. The deviations or percentage deviations were determined by comparing the results of each laboratory to the target defined as the peer-group median after exclusion of outliers, and then the pass rates were calculated based on the criterion of RCPA, DGKL and the allowable total error based on biological variation. Results: Two hundred and thirty-five questionnaires were collected. The number of laboratories testing antithrombin(AT), protein C(PC) and protein S(PS) activity were 194, 63 and 50 respectively. The instruments and reagents were mainly from abroad (more than 96%), the matching rate of which were above 94%. For AT, PC and PS activity testing, there were 30.4%, 33.3%, 34.0% of laboratories did not perform verification assays respectively, and 8.8%, 7.9%, 14.0% of laboratories did not renew calibration curve when the reagent lots were changed. 11.3%, 17.5%, 16.0% of laboratories didn't run internal quality control, and 34.9%, 26.9%, 21.4% of laboratories only performed a single level of quality control. 4.1% of laboratories set the reference intervals of AT activity according to different age groups, and the percentage of that of PC and PS activity were 1.6% and 2.0%. 16.0% of laboratories set the reference interval of PS activity by sex. For normal control materials, the CV of AT, PC and PS activity results were 5.7%-12.9%, 4.2%-7.7% and 18.4%-33.1% while the CV for abnormal level were 13.3%-38.3%, 6.1%-14.4% and 31.5%-34.5% respectively. The pass rate was different when it was judged by different criteria. A suitable criterion for each item should be selected according to the concentration level of quality control materials. Conclusion: The comparability between laboratory results are not satisfactory and in order to promote quality improvement, it is necessary to develop guidelines, organize trainings and establish a national EQA scheme.

[The effects and related risk factors on cataract surgery in Shandong province]

Objective: To explore the efficacy and related risk factors on cataract surgery in Shandong province. Methods: A total of 108 190 cataract surgeries which were reported from 17 cities of Shandong province during January 2013 to December were reviewed. The demographic information, preoperative examination, surgery related information (including date of surgery, surgical methods, and intraoperative complications), and postoperative situations (naked eye visual acuity, curative efficacy after three days, and postoperative complications) were reviewed. Wilcoxon signed-ranks, univariate and orderly multivariate Logistic regression analysis were used according to nature of the data. Results: There were 64 852 female patients (59.9 %) and 43 338 male patients (40.1%) in all 108 190 cases. About 36.5% patients (39 496 cases), the highest proportion, were 71 to 80 years of age, 31.26% patients (33 711 cases) were 61 to 70 years old and 13.6% patients (14 720 cases) were over 81 years old. Visual acuity increased significantly after surgery (Z=165.24, P<0.01). Simple factor Logistic regression analysis showed that preoperative corrected visual acuity less than 0.1 (OR=2.30 95%CI: 0.59 to 1.07), complications (OR=8.50,95% CI: 1.34 to 2.94), congenital cataract (OR=1.69, 95%CI: 0.22 to 0.83), extracapsular cataract extraction (OR=1.99, 95% CI:0.57 to 0.81), postoperative complications in three days (OR=7.46, 95% CI:1.77 to 2.25) were predictors of worse outcome after cataract surgery. Multivariate logistic regression analysis showed that the efficacy of cataract surgery were influenced by history of diabetes (OR=1.79, 95% CI: 0.46 to 0.71), history of hypertension (OR=3.49, 95% CI: 1.07-1.43), postoperative complications in three days (OR=3.91, 95% CI: 1.53 to 1.20) and extracapsular cataract extraction (OR=1.54, 95% CI: 0.20 to 0.66). Young male patients (OR=0.82, 95% CI:-0.28 to -0.12), normal preoperative intraocular pressure (OR=0.79, 95%CI: -0.38 to -0.10) and pupil (OR=0.42, 95% CI:-1.17 to -0.57) were predictors of better outcome. Conclusions: Visual acuity improved significantly after cataract surgery in Shandong province. The efficacy of cataract surgery was influenced by many factors. It is important to control systemic diseases and to choose modern operation method. (Chin J Ophthalmol, 2016, 52: 929-935).

Poor sleep in middle-aged women is not associated with menopause per se

Whether sleep problems of menopausal women are associated with vasomotor symptoms and/or changes in estrogen levels associated with menopause or age-related changes in sleep architecture is unclear. This study aimed to determine if poor sleep in middle-aged women is correlated with menopause. This study recruited women seeking care for the first time at the menopause outpatient department of our hospital. Inclusion criteria were an age ≥40 years, not taking any medications for menopausal symptoms, and no sleeping problems or depression. Patients were assessed with the Pittsburgh Sleep Quality Index (PSQI), modified Kupperman Index (KI), and Menopause Rating Scale (MRS). A PSQI score of <7 indicated no sleep disorder and ≥7 indicated a sleep disorder. Blood specimens were analyzed for follicle-stimulating hormone and estradiol levels. A total of 244 women were included in the study; 103 (42.2%) were identified as having a sleep disorder and 141 as not having one. In addition, 156 (64%) women were postmenopausal and 88 (36%) were not menopausal. Follicle-stimulating hormone and estradiol levels were similar between the groups. Patients with a sleep disorder had a significantly higher total modified KI score and total MRS score (both, P<0.001) compared with those without a sleep disorder. Correlations of the PSQI total score with the KI and MRS were similar in menopausal and non-menopausal women. These results do not support that menopause per se specifically contributes to sleep problems.

Prognostic role of tumor PIK3CA mutation in colorectal cancer: a systematic review and meta-analysis

BACKGROUND

Somatic mutations in the phosphatidylinositol-4,5-bisphosphate 3-kinase/AKT pathway play a vital role in carcinogenesis. Approximately 15%-20% of colorectal cancers (CRCs) harbor activating mutations in PIK3CA, making it one of the most frequently mutated genes in CRC. We thus carried out a systematic review and meta-analysis investigating the prognostic significance of PIK3CA mutations in CRC.

MATERIALS AND METHODS

Electronic databases were searched from inception through May 2015. We extracted the study characteristics and prognostic data of each eligible study. The hazard ratio (HR) and 95% confidence interval (CI) were derived and pooled using the random-effects Mantel-Haenszel model.

RESULTS

Twenty-eight studies enrolling 12 747 patients were eligible for inclusion. Data on overall survival (OS) and progression-free survival (PFS) were available from 19 and 10 studies, respectively. Comparing PIK3CA-mutated CRC patients with PIK3CA-wild-type CRC patients, the summary HRs for OS and PFS were 0.96 (95% CI 0.83-1.12) and 1.20 (95% CI 0.98-1.46), respectively. The trim-and-fill, Copas model and subgroup analyses stratified by the study characteristics confirmed the robustness of the results. Five studies reported the CRC prognosis for PIK3CA mutations in exons 9 and 20 separately; neither exon 9 mutation nor exon 20 mutation in PIK3CA was significantly associated with patient survival.

CONCLUSIONS

Our findings suggest that PIK3CA mutation has the neutral prognostic effects on CRC OS and PFS. Evidence was accumulating for the establishment of CRC survival between PIK3CA mutations and patient-specific clinical or molecular profiles.

[Eccrine angiomatous hamartoma: a clinicalopathologic analysis of 4 cases]

OBJECTIVE

To investigate the clinical and histopathologic features, diagnosis and differential diagnosis of eccrine angiomatous hamartoma(EAH).

METHODS

Four cases of eccrine angiomatous hamartoma were studied by light microscopy and immunohistochemical staining along with review of the literature.

RESULTS

There were 3 male and 1 female patients at diagnosis in age of 4 months, 3.5 years, 5.5 years and 14.0 years, respectively. Tumor sites included the left little finger (1 case), right index finger (1 case), lower back (1 case) and knee (1 case). Clinically, most cases presented as a solitary, flesh or reddish papule, plaque or nodule with size of 0.4-6.0 cm in diameter. The skin lesions in 3 cases enlarged commensurate with the growth of the patients, and local hyperhidrosis in one case. Histologically, EAH was characterized by proliferation of well-differentiated eccrine secretory and ductal elements closely associated with thin-walled angiomatous channels in the middle or deep dermis and subcutaneous tissue. By immunohistochemistry, the vascular components were positive for CD31, CD34 and factor Ⅷ related antigen while the eccrine glands were positive for S-100 protein, CEA, EMA, CAM5.2 and GCDFP15. Local surgical resection was performed in 4 cases and follow-up data (0.5 to 4.5 years) showed no recurrence.

CONCLUSION

EAH is a rare, benign cutaneous hamartoma. Combination of clinical manifestations, histological changes and immunohistochemical findings is useful for the diagnosis and differential diagnosis.

[Evaluation and characterization of the certified reference materials for coagulation factor Ⅷ and Ⅸ activity testing]

OBJECTIVE

To evaluate and characterize the certified reference materials for coagulation factor Ⅷ (FⅧ) and factor Ⅸ (FⅨ) activity testing.

METHODS

The homogeneity and stability of three lots of certified reference materials (F01-F03) with different factor concentrations were evaluated according to guidelines"Reference materials-general and statistical principles for certification","Guidance on evaluating the homogeneity and stability of samples used for proficiency testing"and"Technical Norm of Primary Reference Material". The certified reference materials were characterized by eight laboratories using one-stage method, which were calibrated by the coagulation standard provided by the National Institute for Biological Standards and Control (NIBSC) in UK.

RESULTS

The Coefficient of Variation (CV) of homogeneity test of FⅧ activity of three lots of certified reference materials were 3.9%, 3.3% and 3.4%, respectively. While that of FⅨ activity were 3.7%, 3.0% and 1.8%, respectively. The results of one-way ANOVA showed that all certified reference materials had good homogeneity (P>0.05), and the between-bottle homogeneity uncertainties (ubb) of FⅧ and FⅨ activity were 0.5%-2.9% and 0.1%-3.9%, respectively. All certified reference materials stored in -80 ℃ remained stable in 9 months by trend analysis, and the long-term stability uncertainties(ults) of FⅧ and FⅨ activity were 0.5%-5.1% and 1.3%-4.4%, respectively. The characterization uncertainties (uchar) of FⅧ and FⅨ activity testing were 0.9%-2.4% and 1.1%-2.4%, respectively. The combined uncertainties and extended uncertainties (coverage factor k=2) were calculated. The assigned values of each lot of certified reference materials for FⅧ activity were (85±13)%, (36.0±3.4)% and (20.5±2.3)%, and that were (102±13)%, (47.8±6.9)% and (29.3±3.8)% for FⅨ activity, respectively.

CONCLUSIONS

The certified reference materials for FⅧ and FⅨ activity testing have good homogeneity and stability. The results of the characterization are accurate and reliable.

Multicenter study of autoverification methods of hematology analysis

This study was designed to establish and validate a set of autoverification methods for hematology analysis. One thousand and twenty-four samples were selected from Shanghai Ruijin Hospital and 999 from Beijing Hospital, China. False positive, false negative and autoverification pass rates were verified and the rules were then adjusted and confirmed according to the verification results. After confirmation, at least 10,000 sample cases were selected from Shanghai Ruijin Hospital, Beijing Hospital and China Armed Police General Hospital and checked automatically. The differences in the autoverification pass rate and average report delivery time before and after the application of the autoverification methods were compared between the three hospitals. Preliminary validation results showed that the false negative rates of the Shanghai Ruijin Hospital and Beijing Hospital were less than 2%. The false positive rates of these two hospitals were high, close to 18%. After rule adjustment, the false negative rate was basically the same as before adjustment, but the false positive rate declined obviously while the pass rate of autoverification improved significantly. The autoverification pass rates of the three hospitals were 76.4%, 85.1% and 84.2%, respectively. The turnover time (TAT, time from receipt of sample to report of the result) of the three hospitals decreased by 4.1 min, 8.8 min and 10.2 min, respectively. Autoverification systems using a Mindray BC-6800 auto hematology analyzer and labXpert were confirmed as being effective in reducing TAT and enhancing working efficiency on the premise of ensuring low false negative rate.

Ghrelin attenuates the growth of HO-8910 ovarian cancer cells through the ERK pathway

Ovarian cancer is one of the most common causes of death from gynecologic tumors and is an important public health issue. Ghrelin is a recently discovered bioactive peptide that acts as a natural endogenous ligand of the growth hormone secretagogue receptor (GHSR). Several studies have identified the protective effects of ghrelin on the mammalian reproductive system. However, little research has been done on the effects of ghrelin on ovarian cancer cells, and the underlying mechanisms of these effects. We sought to understand the potential involvement of mitogen-activated protein kinases (MAPKs) in ghrelin-mediated inhibition of growth of the ovarian line HO-8910. We applied different concentrations of ghrelin and an inhibitor of the ghrelin receptor (D-Lys3-GHRP-6) to HO-8910 cells and observed the growth rate of cells and changes in phosphorylation of the MAPKs ERK1/2, JNK and p38. We discovered that ghrelin-induced apoptosis of HO-8910 cells was though phosphorylated ERK1/2, and that this phosphorylation (as well as p90rsk phosphorylation) was mediated by the GHSR. The ERK1/2 pathway is known to play an essential part in the ghrelin-mediated apoptosis of HO-8910 cells. Hence, our study suggests that ghrelin inhibits the growth of HO-8910 cells primarily through the GHSR/ERK pathway.

Mitochondrial ND3 G10398A mutation: a biomarker for breast cancer

Mitochondrial DNA mutations have been found to play important roles in carcinogenesis. The most common G10398A mutation, a non-conservative amino acid substitution from Thr to Ala, seems to be involved in the tumorigenesis of breast cancer. Results from studies concerning this mutation remain inconclusive. In the current study, we first took clinical and molecular datasets from case-control studies to determine the association between the G10398A mutation and breast cancer. We further used the Phylotree to determine the haplogroups of this mutation. The frequencies of this mutation in 500 unrelated healthy controls were also screened. We found that this mutation is very common in the human population, and may be a polymorph.

Error-based extraction of states and energy landscapes from experimental single-molecule time-series

Characterization of states, the essential components of the underlying energy landscapes, is one of the most intriguing subjects in single-molecule (SM) experiments due to the existence of noise inherent to the measurements. Here we present a method to extract the underlying state sequences from experimental SM time-series. Taking into account empirical error and the finite sampling of the time-series, the method extracts a steady-state network which provides an approximation of the underlying effective free energy landscape. The core of the method is the application of rate-distortion theory from information theory, allowing the individual data points to be assigned to multiple states simultaneously. We demonstrate the method's proficiency in its application to simulated trajectories as well as to experimental SM fluorescence resonance energy transfer (FRET) trajectories obtained from isolated agonist binding domains of the AMPA receptor, an ionotropic glutamate receptor that is prevalent in the central nervous system.

Local-heterogeneous responses and transient dynamics of cage breaking and formation in colloidal fluids

Quantifying the interactions in dense colloidal fluids requires a properly designed order parameter. We present a modified bond-orientational order parameter, ψ̄6, to avoid problems of the original definition of bond-orientational order parameter. The original bond-orientational order parameter can change discontinuously in time but our modified order parameter is free from the discontinuity and, thus, it is a suitable measure to quantify the dynamics of the bond-orientational ordering of the local surroundings. Here we analyze ψ̄6 in a dense driven monodisperse quasi-two-dimensional colloidal fluids where a single particle is optically trapped at the center. The perturbation by the trapped and driven particle alters the structure and dynamics of the neighboring particles. This perturbation disturbs the flow and causes spatial and temporal distortion of the bond-orientational configuration surrounding each particle. We investigate spatio-temporal behavior of ψ̄6 by a Wavelet transform that provides a time-frequency representation of the time series of ψ̄6. It is found that particles that have high power in frequencies corresponding to the inverse of the timescale of perturbation undergo distortions of their packing configurations that result in cage breaking and formation dynamics. To gain insight into the dynamic structure of cage breaking and formation of bond-orientational ordering, we compare the cage breaking and formation dynamics with the underlying dynamical structure identified by Lagrangian Coherent Structures (LCSs) estimated from the finite-time Lyapunov exponent (FTLE) field. The LCSs are moving separatrices that effectively divide the flow into distinct regions with different dynamical behavior. It is shown that the spatial distribution of the FTLE field and the power of particles in the wavelet transform have positive correlation, implying that LCSs provide a dynamic structure that dominates the dynamics of cage breaking and formation of the colloidal fluids.

The increase of the functional entropy of the human brain with age

We use entropy to characterize intrinsic ageing properties of the human brain. Analysis of fMRI data from a large dataset of individuals, using resting state BOLD signals, demonstrated that a functional entropy associated with brain activity increases with age. During an average lifespan, the entropy, which was calculated from a population of individuals, increased by approximately 0.1 bits, due to correlations in BOLD activity becoming more widely distributed. We attribute this to the number of excitatory neurons and the excitatory conductance decreasing with age. Incorporating these properties into a computational model leads to quantitatively similar results to the fMRI data. Our dataset involved males and females and we found significant differences between them. The entropy of males at birth was lower than that of females. However, the entropies of the two sexes increase at different rates, and intersect at approximately 50 years; after this age, males have a larger entropy.

Reactivity boundaries for chemical reactions associated with higher-index and multiple saddles

Reactivity boundaries that divide the origin and destination of trajectories are of crucial importance to reveal the mechanism of reactions, which was recently found to exist robustly even at high energies for index 1 saddles [Phys. Rev. Lett. 105, 048304 (2010)]. Here we revisit the concept of the reactivity boundary and propose a more general definition that can involve a single reaction associated with a bottleneck composed of higher-index saddles and/or several saddle points with different indices, where the normal form theory, based on expansion around a single stationary point, does not work. We numerically demonstrate the reactivity boundary by using a reduced model system of the H(5)(+) cation where the proton exchange reaction takes place through a bottleneck composed of two index 2 saddle points and two index 1 saddle points. The cross section of the reactivity boundary in the reactant region of the phase space reveals which initial conditions are effective in making the reaction happen and thus sheds light on the reaction mechanism.

Aggregated markov model using time series of single molecule dwell times with minimum excessive information

Statistics of the dwell times, the stationary state distributions (SSDs), are often studied to infer the underlying kinetics from a single molecule finite-level time series. However, it is well known that the underlying kinetic scheme, a hidden Markov model (HMM), cannot be identified uniquely from the SSDs because some features of the underlying HMM are hidden by finite-level measurements. Here, we quantify the amount of excessive information in a given HMM that is not warranted by the measured SSDs and extract the HMM with minimum excessive information as the most objective representation of the data. The method is applied to a single molecule enzymatic turnover experiment, and the origin of dynamic disorder is discussed in terms of the network properties of the HMM.

Reactivity boundaries to separate the fate of a chemical reaction associated with an index-two saddle

Reactivity boundaries that divide the destination and the origin of trajectories are of crucial importance to reveal the mechanism of reactions. We investigate whether such reactivity boundaries can be extracted for higher index saddles in terms of a nonlinear canonical transformation successful for index-one saddles by using a model system with an index-two saddle. It is found that the true reactivity boundaries do not coincide with those extracted by the transformation taking into account a nonlinearity in the region of the saddle even for small perturbations, and the discrepancy is more pronounced for the less repulsive direction of the index-two saddle system. The present result indicates an importance of the global properties of the phase space to identify the reactivity boundaries, relevant to the question of what reactant and product are in phase space, for saddles with index more than one.

Dynamic disorder in single-enzyme experiments: facts and artifacts

Using a single-molecule fluorescence approach, the time series of catalytic events of an enzymatic reaction can be monitored, yielding a sequence of fluorescent "on"- and "off"-states. An accurate on/off-assignment is complicated by the intrinsic and extrinsic noise in every single-molecule fluorescence experiment. Using simulated data, the performance of the most widely employed binning and thresholding approach was systematically compared to change point analysis. It is shown that the underlying on- and off-histograms as well as the off-autocorrelation are not necessarily extracted from the "signal'' buried in noise. The shapes of the on- and off-histograms are affected by artifacts introduced by the analysis procedure and depend on the signal-to-noise ratio and the overall fluorescence intensity. For experimental data where the background intensity is not constant over time we consider change point analysis to be more accurate. When using change point analysis for data of the enzyme α-chymotrypsin, no characteristics of dynamic disorder was found. In light of these results, dynamic disorder might not be a general sign of enzymatic reactions.

Electrical stimulation affects metabolic enzyme phosphorylation, protease activation, and meat tenderization in beef

The objective of this study was to investigate the response of sarcoplasmic proteins in bovine LM to low-voltage electrical stimulation (ES; 80 V, 35 s) after dressing and its contribution to meat tenderization at an early postmortem time. Proteome analysis showed that ES resulted in decreased (P < 0.05) phosphorylation of creatine kinase M chain, fructose bisphosphate aldolase C-A, β-enolase, and pyruvate kinase at 3 h postmortem. Zymography indicated an earlier (P < 0.05) activation of μ-calpain in ES muscles. Free lysosomal cathepsin B and L activity increased faster (P < 0.05) in ES muscles up to 24 h. Immunohistochemistry and transmission electron microscopy further indicated that lysosomal enzymes were released at an early postmortem time. Electrical stimulation also induced ultrastructural disruption of sarcomeres. In addition, ES accelerated (P < 0.05) the depletion of ATP, creatine phosphate, and glycogen, as well as a pH decline and the more preferred pH/temperature decline mode. Finally, ES accelerated meat tenderization, resulting in lesser (P < 0.05) shear force values than the control over the testing time. A possible relationship was suggested between a change in the phosphorylation of energy metabolic enzymes and the postmortem tenderization of beef. Our results suggested the possible importance of the activation of μ-calpain, phosphorylation of sarcoplasmic proteins, and release of lysosomal enzymes for ES-induced tenderization of beef muscle.

Toward sub-20 nm hybrid nanofabrication by combining the molecular ruler method and electron beam lithography

It is of great interest and importance to develop new nanofabrication processes to fabricate sub-20 nm structures with sub-2 nm resolution for next-generation nanoelectronic devices. A combination of electron beam lithography (EBL) and a molecular ruler is one of the promising methods to make these fine structures. Here we successfully develop a hybrid method to fabricate sub-20 nm nanogap devices at the desired positions with a complex structure by developing a post-EBL process, which enabled us to avoid damaging the molecular ruler with the high-energy electron beam, and to fully utilize the EBL resolution. It was found that slight etching of the Ti adhesion layer of the parent metal (Pt) by ACT935J solution assisted the removal of molecular rulers, resulting in improved enhancement in the product yield (over 70%) of nanogap devices.

Cooperativity at different space and time scales in multiscale protein dynamics

A method proposed by Matsunaga [Phys. Rev. Lett. 99, 238103 (2007)] is applied to simple stochastic models and two model proteins composed of 46 amino beads with three different kinds of residues. The method, which is based on the combination of the principal component analysis and the finite size Lyapunov exponent, characterize the coarse-grained dynamics in different spatiotemporal hierarchies in protein dynamics. The application of the method to model proteins reveals that the low-indexed (large-variance) principal components carry less-divergent, regularized dynamics at the coarse-grained scales on a less-frustrated energy landscape, whereas this less-divergent nature is less pronounced for a protein model with a more frustrated energy landscape. It is also revealed that our technique can differentiate the collective motions on the projected principal component space inherent to the system and the apparent collective behavior which can appear even in high-dimensional stochastic systems.

Effects of low-voltage electrical stimulation and rapid chilling on meat quality characteristics of Chinese Yellow crossbred bulls

In this study, the effects of low-voltage electrical stimulation (LVES) and rapid chilling (RC) treatments on the quality characteristics of beef carcasses were evaluated, including the rate of pH and temperature decline, evaporative loss of carcasses, purge loss, cooking loss, and shear force values of m. longissimus steaks. Each carcass of 28 Chinese Yellow crossbred (SimmentalxYanbian) bulls was subjected to one of the four treatments, i.e., electrical stimulation and conventional chilling (ES/NR), electrical stimulation and rapid chilling (ES/RC), no electrical stimulation and rapid chilling (NE/RC), or no electrical stimulation and conventional chilling (NE/NR). Carcass pH and temperature were measured at 1, 3, 5, 7, 9, 11, and 24h post-mortem. After that, a 2.5-cm-thick m. longissimus steak was taken from the right side of each carcass and used for analyses of purge loss, cooking loss and Warner-Bratzler shear force (WBSF). The results showed that LVES accelerated the rate of carcass pH decline (P<0.05) and rapid chilling increased the rate of carcass temperature decline (P<0.05). There was no significant difference found for the mean carcass evaporative losses from all treatments (P>0.05). Mean purge losses for m. longissimus steaks from rapidly chilled carcasses were lower (P<0.05) than those from conventionally chilled carcasses. Electrical stimulation had no impact on m. longissimus steak purge losses (P>0.05). Rapid chilling significantly decreased (P<0.05) the cooking loss of m. longissimus steaks from electrically stimulated carcasses whilst it increased the cooking loss of m. longissimus steaks from carcasses without stimulation (P<0.05). LVES increased (P<0.05) cooking loss of m. longissimus steaks from conventionally chilled carcasses, but had no effect under the procedure of pre-rigor rapid chilling (P>0.05). The lowest mean shear force value was found for the ES/NR-treated m. longissimus steaks, whilst the highest one for the NE/RC-treated carcasses (P<0.05). Regression analyses indicated that carcass pH at 1h post-mortem was the most useful predictor for beef shear force. Abattoirs processing Chinese Yellow bulls could optimize meat quality by using low-voltage stimulation together with pre-rigor rapid chilling.