Identification of QTLs associated with seed protein concentration in two diverse recombinant inbred line populations of pea

Improving the seed protein concentration (SPC) of pea (Pisum sativum L.) has turned into an important breeding objective because of the consumer demand for plant-based protein and demand from protein fractionation industries. To support the marker-assisted selection (MAS) of SPC towards accelerated breeding of improved cultivars, we have explored two diverse recombinant inbred line (RIL) populations to identify the quantitative trait loci (QTLs) associated with SPC. The two RIL populations, MP 1918 × P0540-91 (PR-30) and Ballet × Cameor (PR-31), were derived from crosses between moderate SPC × high SPC accessions. A total of 166 and 159 RILs of PR-30 and PR-31, respectively, were genotyped using an Axiom® 90K SNP array and 13.2K SNP arrays, respectively. The RILs were phenotyped in replicated trials in two and three locations of Saskatchewan, Canada in 2020 and 2021, respectively, for agronomic assessment and SPC. Using composite interval mapping, we identified three QTLs associated with SPC in PR-30 and five QTLs in PR-31, with the LOD value ranging from 3.0 to 11.0. A majority of these QTLs were unique to these populations compared to the previously known QTLs for SPC. The QTL SPC-Ps-5.1 overlapped with the earlier reported SPC associated QTL PC-QTL-3. Three QTLs, SPC-Ps-4.2, SPC-Ps-5.1, and SPC-Ps-7.2 with LOD scores of 7.2, 7.9, and 11.3, and which explained 14.5%, 11.6%, and 11.3% of the phenotypic variance, respectively, can be used for marker-assisted breeding to increase SPC in peas. Eight QTLs associated with the grain yield were identified with LOD scores ranging from 3.1 to 8.2. Two sets of QTLs, SPC-Ps-2.1 and GY-Ps-2.1, and SPC-Ps-5.1 and GY-Ps-5.3, shared the QTL/peak regions. Each set of QTLs contributed to either SPC or grain yield depending on which parent the QTL region is derived from, thus confirming that breeding for SPC should take into consideration the effects on grain yield.

Exploring the functional attributes and in vitro starch and protein digestibility of pea flours having a wide range of amylose content

In this study, ten pea flours covering a broad range of amylose content (37.2-77.6 %, dsb) were characterized for functional and nutritional properties. As the amylose contents increased, the starch contents of the pea flours showed a downward trend (r = -0.990, p < 0.001 in Pearson correlation) but their protein and total dietary fiber contents exhibited an upward trend (r = 0.915, p < 0.001 and r = 0.885, p < 0.001, respectively). A greater amylose content tended to increase starch gelatinization temperatures of the pea flours, which thus required a higher cooking temperature for pasting viscosity development and subsequent gel formation. An increased amylose level reduced in vitro starch digestibility of the cooked pea flours (r = -0.944, p < 0.001) but did not influence in vitro protein digestibility. The insightful findings will be valuable for utilizing the diverse pea lines to create new flour, starch, and protein ingredients.

Understanding Starch Metabolism in Pea Seeds towards Tailoring Functionality for Value-Added Utilization

Starch is the most abundant storage carbohydrate and a major component in pea seeds, accounting for about 50% of dry seed weight. As a by-product of pea protein processing, current uses for pea starch are limited to low-value, commodity markets. The globally growing demand for pea protein poses a great challenge for the pea fractionation industry to develop new markets for starch valorization. However, there exist gaps in our understanding of the genetic mechanism underlying starch metabolism, and its relationship with physicochemical and functional properties, which is a prerequisite for targeted tailoring functionality and innovative applications of starch. This review outlines the understanding of starch metabolism with a particular focus on peas and highlights the knowledge of pea starch granule structure and its relationship with functional properties, and industrial applications. Using the currently available pea genetics and genomics knowledge and breakthroughs in omics technologies, we discuss the perspectives and possible avenues to advance our understanding of starch metabolism in peas at an unprecedented level, to ultimately enable the molecular design of multi-functional native pea starch and to create value-added utilization.

[The association between serum bilirubin levels and hearing loss in the patients with bilateral sudden deafness]

Objective:The aim of this study was to investigate the association between serum bilirubin levels and the severity of bilateral sudden sensorineural hearing loss （BSSHL）. Method:A total of 113 patients with bilateral axillary sputum were enrolled, and the relationship between serum bilirubin levels and initial hearing levels was explored using a univariate and multivariate linear regression model. Result:Compared with the group with moderate and below hearing loss （≤70 dB HL）, patients with severe profound HL（>70 dB HL） were more likely to have lower levels of total and indirect bilirubin level, magnesium and relative hearing gain, higher levels of final hearing, white blood counts, neutrophil, platelet and alkaline phosphatase. After adjusting for possible confounders, only serum indirect bilirubin levels were significantly negatively correlated with initial hearing loss in patients with bilateral axillary sputum. 1 μmol/L increase of IBIL was associated with 1.1 dB （95%CI: -2.2, 0.0） reduction in initial hearing loss. Conclusion:Within the normal or mildly elevated range, higher levels of IBIL are independently and significantly associated with less severe hearing loss in BSSHL. It suggested a beneficial effect of bilirubin on auditory system.

[Classification of sudden deafness prognosis based on deep learning method]

Objective:This study aimed to develop predictive models for sudden sensorineural hearing loss through deep belief network (DBN) and explore whether the model performances differ when adopting different outcome criteria. Method: 228 potential predictors involving the clinical characteristics, audio logical data, and serological parameters out of 1 220 hospitalized SSHL patients who were admitted from June 2008 to December 2015 were analyzed retrospectively. The hearing data of sudden deafness were classified into two or four categories based on Chinese criteria and Siegel criteria, which were used to develop the DBN models. The area under the receiver operating characteristic curve (ROC-AUC) and accuracy were used to compare the predictive performance of different models. Result: The DBN model developed for predicting the dichotomized outcomes had better performance than that of the fourcategory outcomes. When the iteration number reached 500 times, DBN model constructed for prediction of dichotomized outcomes based on Siegel's criteria had demonstrated the best performance with an accuracy of 76.25% and an AUC of 0.81. According to indices from first layer weights, DBN gave a rank of top 10 sensitive features for hearing outcome prediction focusing on indicators regarding coagulation, demographics and pre-treatment hearing levels independent of the outcome assessment criteria. Conclusion: DBN provides a robust outcome prediction ability in SSHL datasets with rich and complex variables, especially when utilized to predict dichotomized outcomes based on the Siegel criteria. In addition, this advanced deep learning technique can automatically extract valuable predictors, which is consistent with those that had been verified in previous studies by traditional statistical methods. This study provides further evidence for extending the use of DBN algorithm to the field of developing prediction or classification models for other otological diseases in the future..

Predicting the hearing outcome in sudden sensorineural hearing loss via machine learning models

OBJECTIVE

Sudden sensorineural hearing loss (SSHL) is a multifactorial disorder with high heterogeneity, thus the outcomes vary widely. This study aimed to develop predictive models based on four machine learning methods for SSHL, identifying the best performer for clinical application.

DESIGN

Single-centre retrospective study.

SETTING

Chinese People's liberation army (PLA) hospital, Beijing, China.

PARTICIPANTS

A total of 1220 in-patient SSHL patients were enrolled between June 2008 and December 2015.

MAIN OUTCOME MEASURES

An advanced deep learning technique, deep belief network (DBN), together with the conventional logistic regression (LR), support vector machine (SVM) and multilayer perceptron (MLP) were developed to predict the dichotomised hearing outcome of SSHL by inputting six feature collections derived from 149 potential predictors. Accuracy, precision, recall, F-score and the area under the receiver operator characteristic curves (ROC-AUC) were exploited to compare the prediction performance of different models.

RESULTS

Overall the best predictive ability was provided by the DBN model when tested in the raw data set with 149 variables, achieving an accuracy of 77.58% and AUC of 0.84. Nevertheless, DBN yielded inferior performance after feature pruning. In contrast, the LR, SVM and MLP models demonstrated opposite trend as the greatest individual prediction powers were obtained when included merely three variables, with the ROC-AUC ranging from 0.79 to 0.81, and then decreased with the increasing size of input features combinations.

CONCLUSIONS

With the input of enough features, DBN can be a robust prediction tool for SSHL. But LR is more practical for early prediction in routine clinical application using three readily available variables, that is time elapse between symptom onset and study entry, initial hearing level and audiogram.

Hot water molecules from dissociative recombination of D3O+ with cold electrons

Individual product channels in the dissociative recombination of deuterated hydronium ions and cold electrons are studied in an ion storage ring by velocity imaging using spatial and mass-sensitive detection of the neutral reaction fragments. Initial and final molecular excitation are analyzed, finding the outgoing water molecules to carry internal excitation of more than 3 eV in 90% of the recombination events. Initial rotation is found to be substantial and in three-body breakup strongly asymmetric energy repartition among the deuterium products is enhanced for hot parent ions.

Quantitative trait loci for lodging resistance, plant height and partial resistance to mycosphaerella blight in field pea (Pisum sativum L.)

With the development of genetic maps and the identification of the most-likely positions of quantitative trait loci (QTLs) on these maps, molecular markers for lodging resistance can be identified. Consequently, marker-assisted selection (MAS) has the potential to improve the efficiency of selection for lodging resistance in a breeding program. This study was conducted to identify genetic loci associated with lodging resistance, plant height and reaction to mycosphaerella blight in pea. A population consisting of 88 recombinant inbred lines (RILs) was developed from a cross between Carneval and MP1401. The RILs were evaluated in 11 environments across the provinces of Manitoba, Saskatchewan and Alberta, Canada in 1998, 1999 and 2000. One hundred and ninety two amplified fragment length polymorphism (AFLP) markers, 13 random amplified polymorphic DNA (RAPD) markers and one sequence tagged site (STS) marker were assigned to ten linkage groups (LGs) that covered 1,274 centi Morgans (cM) of the pea genome. Six of these LGs were aligned with the previous pea map. Two QTLs were identified for lodging resistance that collectively explained 58% of the total phenotypic variation in the mean environment. Three QTLs were identified each for plant height and resistance to mycosphaerella blight, which accounted for 65% and 36% of the total phenotypic variation, respectively, in the mean environment. These QTLs were relatively consistent across environments. The AFLP marker that was associated with the major locus for lodging resistance was converted into the sequence-characterized amplified-region (SCAR) marker. The presence or absence of the SCAR marker corresponded well with the lodging reaction of 50 commercial pea varieties.

Neonatal pulmonary function testing

Recent advances in technology have made it possible for use to measure neonatal pulmonary function, even in very small infants. Applying PM measurement as a tool for ventilator-patient management improves outcome in the NICU. With PFT in the laboratory, we can diagnose and determine severity of pulmonary illness and evaluate therapies through infancy and childhood. Although the task of safely measuring pulmonary function in infants can be daunting, there is no reason why more PFT labs should not offer services to these patients.

Large-scale DRB and DQB1 oligonucleotide typing for the NMDP registry: progress report from year 2

DNA typing of HLA class II alleles of the DRB1/3/4/5 and DQB1 loci using sequence-specific oligonucleotide probes and polymerase chain reaction amplified DNA has been used for the large-scale typing of donors for the National Marrow Donor Program unrelated donor registry. The results of quality control analysis for the second year of the project (10/1/939/30/94) show the typing continues to be highly accurate, specific, and reliable. The average percent of correctly classified HLA oligotypes (groups of alleles defined by a hybridization pattern with a panel of sequence-specific oligonucleotide probes) based on 9,244 DRB1 and 7,244 DQB1 assignments was 99.8% (range 99.4%100.0%) for DRB1/DRB3/DRB4/DRB5 and 99.8% (range 99.6%100.0%) for DQB1. This level of accuracy is particularly remarkable because the 4,636 DRB quality control samples were tested blindly and could not be distinguished from 57,580 donor samples tested at the same time by the laboratories.

Long distance telephone fraud and abuse

The article discusses the difference between abuse and fraud, the cost of fraud to a business, how fraud is accomplished, and ways to combat long distance fraud.

HLA-DQB1 allele typing by a new PCR-RFLP method: Correlation with a PCR-SSO method

We have developed a new PCR-RFLP method for HLA-DQB1 typing. This method was easy to follow, requiring only one DQB1 generic amplification and 5 endonucleases to assign 14 out of 15 HLA-DQB1 alleles. In addition, we determined that by using one generic amplification and two enzymes (Sau96 I and Hae III) it was possible to type the generic specificities: DQw2, DQw4, DQw5, DQw6, and DQw7, DQw8-9, providing a practical alternative for serological HLA-DQ generic typing. We also performed a side-by-side correlation with a PCR-SSO typing method and found an almost 100% concordance between the methods. The limitations of these methods were: 1) the PCR-RFLP method did not allow the differentiation between the HLA-DQB1*0602 and *0603 alleles; 2) the PCR-SSO method gave crosshybridization signals in the detection of *0302 or *0303 alleles. Our results suggested that both methods, PCR-RFLP and PCR-SSO, are useful alternatives for HLA-DQB1 typing.

Paramyosin inhibits complement C1

We report here the results of studies showing that inhibition of C is a property of several invertebrate paramyosins. Paramyosins from Taenia solium, Schistosoma mansoni, and the mussel Mytilus edulis bind polymeric collagen and can be isolated from crude extracts of tissues by collagen affinity. These paramyosins inhibit C1 function whether the C1 is isolated or present in C2-deficient serum. Because T. solium paramyosin was the best inhibitor, we concentrated further studies on this molecule. T. solium paramyosin binds purified C1q in solution with a dose/response similar to C1r2S2. Further studies of the C1-paramyosin interaction indicate that: 1) C4 is not activated, 2) C4b2a decay is not affected, and 3) there is no effect on the efficiency of C3-9, as provided in EDTA-chelated guinea pig serum, in lysing SRBC. Thus, paramyosin inhibition is directed at the initiation of the classical pathway. The results suggest that paramyosins of helminthic parasites may have a role as modulators of the host immune response through C inhibition at C1.

Paramyosin inhibits complement C1

We report here the results of studies showing that inhibition of C is a property of several invertebrate paramyosins. Paramyosins from Taenia solium, Schistosoma mansoni, and the mussel Mytilus edulis bind polymeric collagen and can be isolated from crude extracts of tissues by collagen affinity. These paramyosins inhibit C1 function whether the C1 is isolated or present in C2-deficient serum. Because T. solium paramyosin was the best inhibitor, we concentrated further studies on this molecule. T. solium paramyosin binds purified C1q in solution with a dose/response similar to C1r2S2. Further studies of the C1-paramyosin interaction indicate that: 1) C4 is not activated, 2) C4b2a decay is not affected, and 3) there is no effect on the efficiency of C3-9, as provided in EDTA-chelated guinea pig serum, in lysing SRBC. Thus, paramyosin inhibition is directed at the initiation of the classical pathway. The results suggest that paramyosins of helminthic parasites may have a role as modulators of the host immune response through C inhibition at C1.

Neonatal high-frequency jet ventilation

Ten neonates with intractable respiratory failure were treated with high-frequency jet ventilation (HFJV). Nine had progressive pulmonary air leaks with either bronchopleural fistulas or pulmonary interstitial emphysema as the primary cause of their respiratory failure. Following HFJV, x-ray film evidence of pulmonary air leaks decreased in seven of the nine neonates. PaO2/FIO2 increased in eight of the ten patients (P less than .05), and PaCO2 values decreased in nine of the ten patients (P less than .01). Five patients survived. Three of the six patients exposed to HFJV for more than 20 hours developed significant tracheal obstruction. From this experience, it may be concluded that HFJV can successfully ventilate certain neonates with intractable respiratory failure secondary to progressive pulmonary air leaks. In its present form, long-term neonatal HFJV carries a risk of airway obstruction and/or damage.

m-[o-(2-Chloro-5-Fluorosulfonylphenylureido)Phenoxybutoxy]Benzamidine: Affinity Labeling Reagent Which Can Identify Secondary Binding Sites of Coagulation Complement and Fibrinolytic Serine Proteases

We have determined that m-[o-(2-chloro-5-fluorosulfonylphenylureido)phenoxybutoxy]benza-midine [mCP(PBA)-F] is an affinity labeling reagent which labels both polypeptide chains of thrombin, factor Xa, complement component CIS and plasmin. As this means it is reacting outside of the catalytic center, we have called this reagent an exo-site affinity labeling reagent. Progressive irreversible inhibition of these enzymes by this reagent is rapid (k1st 2.5-4.6 x 10-3sec-1), the kinetics of inactivation are consistent with inhibition proceding via formation of a specific enzyme-inhibitor complex analogous to a Michaelis-Menton complex (KL - 115-26 μM), and diisopropylfluorophosphate or p-amidino-phenylmethanesulfonyfluoride Prevent labeling by [3H]mCP(PBA)-F. A molecular model of mCP(PBA)-F shows that the reactive SO2F group can be 17 A from the cationic amidine. The data are consistent with the hypothesis that both peptide chains are required for the specific proteolytic activity exhibited by these proteases and that the peptide chain which does not contain the active site serine is close to the catalytic center. (Supported by NIH and AHA grants