Physiological and symbiotic variation of a long-term evolved Rhizobium strain under alkaline condition.

Physiological variation and adaptation of the long-term evolved rhizobia to alkaline environments where no host plant existence and the stability of their symbiotic properties when they are reinoculated to legume host remain unclear. A highly effective N2-fixing Rhizobium yanglingense strain CCBAU 01603 was used as the ancestral strain and was cultured continuously with/without addition of extra alkaline reagent (KOH) in laboratory conditions for approximately 500 generations. Total 60 evolved clones obtained were checked for their adaptation to higher alkaline pH level and inoculated to their host plant Caragana microphylla to evaluate their symbiotic efficiencies. Most of the evolved clones showed increased adaptation to higher alkaline pH but all of them decreased symbiotic efficiencies, resulting in the formation of irregular root nodules with lower nitrogenase activity, production of abnormal bacteroids, and accumulation more starch grains in uninfected nodule cells. Further demonstration of lower symbiotic efficiencies came from the down-regulated expression of genes related to nitrogen fixation in the bacteroids by transcriptome comparison. In addition, genes related to transporters and other diverse functions were up- or down-regulated in the evolved clones in free-living conditions (like yjiS gene) or in symbiotic situations, demonstrating the significant variations in cellular physiology and symbiosis. Our study revealed that the enhancement of alkaline adaptation but loss of symbiotic efficiencies of the evolved clones had happened during the long-term evolution in alkaline environments where no selective pressures from host plant, offering new insight into the molecular mechanism and direction of rhizobial evolution in nature.

Deep Learning for Accurate Diagnosis of Liver Tumor Based on Magnetic Resonance Imaging and Clinical Data.

Background: Early-stage diagnosis and treatment can improve survival rates of liver cancer patients. Dynamic contrast-enhanced MRI provides the most comprehensive information for differential diagnosis of liver tumors. However, MRI diagnosis is affected by subjective experience, so deep learning may supply a new diagnostic strategy. We used convolutional neural networks (CNNs) to develop a deep learning system (DLS) to classify liver tumors based on enhanced MR images, unenhanced MR images, and clinical data including text and laboratory test results. Methods: Using data from 1,210 patients with liver tumors (N = 31,608 images), we trained CNNs to get seven-way classifiers, binary classifiers, and three-way malignancy-classifiers (Model A-Model G). Models were validated in an external independent extended cohort of 201 patients (N = 6,816 images). The area under receiver operating characteristic (ROC) curve (AUC) were compared across different models. We also compared the sensitivity and specificity of models with the performance of three experienced radiologists. Results: Deep learning achieves a performance on par with three experienced radiologists on classifying liver tumors in seven categories. Using only unenhanced images, CNN performs well in distinguishing malignant from benign liver tumors (AUC, 0.946; 95% CI 0.914-0.979 vs. 0.951; 0.919-0.982, P = 0.664). New CNN combining unenhanced images with clinical data greatly improved the performance of classifying malignancies as hepatocellular carcinoma (AUC, 0.985; 95% CI 0.960-1.000), metastatic tumors (0.998; 0.989-1.000), and other primary malignancies (0.963; 0.896-1.000), and the agreement with pathology was 91.9%.These models mined diagnostic information in unenhanced images and clinical data by deep-neural-network, which were different to previous methods that utilized enhanced images. The sensitivity and specificity of almost every category in these models reached the same high level compared to three experienced radiologists. Conclusion: Trained with data in various acquisition conditions, DLS that integrated these models could be used as an accurate and time-saving assisted-diagnostic strategy for liver tumors in clinical settings, even in the absence of contrast agents. DLS therefore has the potential to avoid contrast-related side effects and reduce economic costs associated with current standard MRI inspection practices for liver tumor patients.

Evolutionarily Conserved nodE, nodO, T1SS, and Hydrogenase System in Rhizobia of Astragalus membranaceus and Caragana intermedia.

Mesorhizobium species are the main microsymbionts associated with the medicinal or sand-fixation plants Astragalus membranaceus and Caragana intermedia (AC) in temperate regions of China, while all the Mesorhizobium strains isolated from each of these plants could nodulate both of them. However, Rhizobium yanglingense strain CCBAU01603 could nodulate AC plants and it's a high efficiency symbiotic and competitive strain with Caragana. Therefore, the common features shared by these symbiotic rhizobia in genera of Mesorhizobium and Rhizobium still remained undiscovered. In order to study the genomic background influencing the host preference of these AC symbiotic strains, the whole genomes of two (M. silamurunense CCBAU01550, M. silamurunense CCBAU45272) and five representative strains (M. septentrionale CCBAU01583, M. amorphae CCBAU01570, M. caraganae CCBAU01502, M. temperatum CCBAU01399, and R. yanglingense CCBAU01603) originally isolated from AC plants were sequenced, respectively. As results, type III secretion systems (T3SS) of AC rhizobia evolved in an irregular pattern, while an evolutionarily specific region including nodE, nodO, T1SS, and a hydrogenase system was detected to be conserved in all these AC rhizobia. Moreover, nodO was verified to be prevalently distributed in other AC rhizobia and was presumed as a factor affecting the nodule formation process. In conclusion, this research interpreted the multifactorial features of the AC rhizobia that may be associated with their host specificity at cross-nodulation group, including nodE, nodZ, T1SS as the possible main determinants; and nodO, hydrogenase system, and T3SS as factors regulating the bacteroid formation or nitrogen fixation efficiency.

Visible light nonlinear absorption and optical limiting of ultrathin ZrSe3 nanoflakes.

The nonlinear absorption and nonlinear refractive properties of ZrSe3 nanoflakes were studied with a 6.5 ns pulse laser at 532 nm. Open-aperture Z-scan curves reveal that ZrSe3 nanoflakes have a strong reverse saturable absorption property, and close-aperture Z-scan curves show that ZrSe3 dispersions possess a positive nonlinear refractive index caused by self-focusing. The nonlinear absorption coefficient, the nonlinear refraction coefficient, and the figures of merit (FOM) of ZrSe3 dispersed in water with linear transmittances of 0.86 at input energy of 18 µJ are 6.35 × 10-10 m W-1 15.73 × 10-17 m2 W-1, and 10.09 × 10-11 esu · cm respectively. In addition, nonlinear optical (NLO) performance of ZrSe3 nanoflakes depends on organic solvent dispersions. ZrSe3 nanoflakes in water dispersions have the largest FOM of 10.27 × 10-11 esu · cm, while the FOM in ethanol dispersions is 5.41 × 10-11 esu · cm at the same input energy of 26.5 µJ. The optical limiting threshold Fth of ZrSe3 nanosheet is 2.2 J cm-2 under picosecond laser pulse. The Results imply that ZrSe3 nanoflakes are an extraordinarily promising material for novel nanophotonic devices like optical limiters.

Reverse saturable absorption and nonlinear refraction of ultrathin ZrS3 nanobelts.

The nonlinear optical (NLO) properties of a ZrS3 nanobelt were measured with a 6.5 ns pulse laser at 532 nm. Its optical response to the incident light exhibits good optical absorptive and refractive effects, with the nonlinear absorption coefficient ß = 4.42 × 10(-10) m W(-1) and the nonlinear refraction coefficient γ = 5.86 × 10(-17) m(2) W(-1) for the ZrS3 nanobelt in ethanol dispersions at an input energy of 34.25 µJ. In addition, the ß values and γ values have dependence on input energy. Results show that the ZrS3 nanobelts have an excellent reverse saturable absorption (RSA) performance in nanosecond pulses, demonstrating that ZrS3 nanobelts are an extraordinarily promising novel optical power limiting material. Meanwhile, compared to the pure ZrS3, graphene oxide (GO) and reduced graphene oxide (RGO), composites (ZrS3/GRO) exhibit an enhanced nonlinear absorption response at the same input energy.

Mutation analysis of the PAH gene in children with phenylketonuria from the Qinghai area of China / 中国当代儿科杂志

<p><b>OBJECTIVE</b>To study the mutation characteristics of the phenylalanine hydroxylase (PAH) gene in children with phenylketonuria (PKU) from the Qinghai area of China, in order to provide basic information for genetic counseling and prenatal diagnosis.</p><p><b>METHODS</b>Mutations of the PAH gene were detected in the promoter and exons 1-13 and their flanking intronic sequences of PAH gene by PCR and DNA sequencing in 49 children with PKU and their parents from the Qinghai area of China.</p><p><b>RESULTS</b>A total of 30 different mutations were detected in 80 out of 98 mutant alleles (82%), including 19 missense (63%), 5 nonsense (17%), 3 splice-site (10%) and 3 deletions (10%). Most mutations were detected in exons 3, 6, 7, 11 and intron 4 of PAH gene. The most frequent mutations were p.R243Q (19%), IVS4-1G>A (9%), p.Y356X (7%) and p.EX6-96A>G(5%). Two novel mutations p.N93fsX5 (c.279-282delCATC) and p.G171E (c.512G>A) were found. p.H64fsX9(c.190delC) was documented for the second time in Chinese PAH gene. The mutation spectrum of the gene PAH in the Qinghai population was similar to that in other populations in North China while significantly different from that in the populations from some provinces in southern China, Japan and Europe.</p><p><b>CONCLUSIONS</b>The mutations of PAH gene in the Qinghai area of China demonstrate a unique diversity, complexity and specificity.</p>

Analysis of mutations in exon 7 of phenylalanine hydroxylase gene among children with phenylketonuria in Ningxia, China / 中国当代儿科杂志

<p><b>OBJECTIVE</b>To investigate the type and frequency of mutations in exon 7 of phenylalanine hydroxylase (PAH) gene among children with phenylketonuria (PKU) in Ningxia, China and to provide a basis for the genetic diagnosis and prenatal diagnosis of PKU in this region.</p><p><b>METHODS</b>Direct sequencing of PCR product was performed to analyze the sequences of exon 7 and its flanking introns of 146 PAH alleles in 73 children with typical PKU (39 cases of Hui nationality and 34 cases of Han nationality) in Ningxia.</p><p><b>RESULTS</b>Six mutations were detected, including R243Q (14.4%), R241C (6.8%), IVS7+2T→A (2.7%), L255S (0.7%), G247V (0.7%), and G247R (0.7%). The overall frequency of mutations (missense mutation and splice site mutation) in exon 7 was 26.0% (38/146). The detection rate of R241C mutation was significantly higher in children of Hui nationality than in children of Han nationality(10% vs 3%; P<0.05).</p><p><b>CONCLUSIONS</b>In Ningxia, R243Q mutation in exon 7 of PAH gene is most common in children with PKU, followed by R241C. The frequency of R241C mutation in exon 7 of PAH gene varies between children with PKU of Hui and Han nationality.</p>

Sperm DNA damage in young men working on the plateau / 中华男科学杂志

<p><b>OBJECTIVE</b>To investigate whether long working in the high-altitude area can damage sperm DNA in men.</p><p><b>METHODS</b>We enlisted 51 service men stationed on the plateau in an observation group and another 53 living in the low-altitude area in a control group. We detected and compared the damages to sperm DNA in the semen samples from the two groups using single cell gel electrophoresis and the sperm chromatin dispersion test.</p><p><b>RESULTS</b>The percentages of total, G1, G2 and G3 comet cells and abnormal sperm of the observation group were (5.56 +/- 3.98)%, (3.72 +/- 1.85)%, (1.57 +/- 1.07)%, (0.27 +/- 0.34)% and (16.59 +/- 12.07)%, respectively, before stationed on the plateau, but significantly increased at 6 months of plateau life ([11.15 +/- 8.59]%, [5.97 +/- 3.26]%, [3.83 +/- 2.13%, [1.35 +/- 1.53]% and [22.03 +/- 15.33]%, P<0.05). The percentages of G2 comet cells and abnormal sperm were decreased to (3.32 +/- 1.83)% and (20.54 +/- 15.52)% at 12 months, but still significantly higher than the baseline (P<0.05).</p><p><b>CONCLUSION</b>Long working on the plateau may damage sperm DNA, but its influence on male fertility deserves further investigation. Therefore, it is important to reinforce reproductive health protection for males working on the plateau.</p>

Characteristics of the PAH gene mutation in Chinese patients with phenylketonuria in Xinjiang / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To study the characteristics of the PAH gene mutation in patients with phenylketonuria (PKU) in Xinjiang area.</p><p><b>METHODS</b>The mutations in exons 3, 5, 6, 7, 11 and 12 and the flanking intronic sequence of the PAH gene were detected by PCR/SSCP analysis and direct DNA sequencing in 46 PKU patients.</p><p><b>RESULTS</b>Twenty different mutations were found in 68/92 alleles (73.9%). The prevalent mutations of R243Q, EX6 96A>G, R111X, Y356X and V399V were similar to that of Northern China populations. The mutations F161S, L255S, P281L, and R413P were significantly different from that in other Chinese populations. It was the second time that E280G and A434D mutations were reported in the world, that L255S, P281L, R261Q, and I65T mutations were found in China. Thirteen different mutations were first found in Chinese Uygur, which showed a distinct ethnic characteristics.</p><p><b>CONCLUSION</b>The study showed not only a distinct and conservative, but also a crossed and syncretic genetic characteristics in Xinjiang Uygur population. The results suggest that Xinjiang could be an ideal genetic resource repertoire for studying diversity of gene mutations, heterogeneity of PAH gene, human origins and migration.</p>

Semen analysis of sterile patients among occupational computermen / 中华男科学杂志

<p><b>OBJECTIVE</b>To explore temn possible correlation between the computer occupational semen quality.</p><p><b>METHODS</b>We included in this study 224 sterile males (118 computermen and 106 non-computermen) treated in our clinic of male sterility and 125 normal fertile men as controls, and analyzed such parameters as semen liquefaction time and sperm density, vitality and motility according to the WHO standard.</p><p><b>RESULTS</b>Compared with the normal controls, there was a significant decrease in the semen volume and sperm density, vitality and motility (P < 0.05-0.01) and a marked increase in liquefaction time in the infertile computermen and non-computermen (P < 0.01). The semen volume and sperm vitality and motility were significantly lower in the infertile computermen than in the infertile non-eomputermen (P < 0.05). The three parameters were also significantly decreased in the 0-5, 6-10 and > 10 h/d computer use groups. Similarly, significantly lower sperm density, vitality and motility were observed in the > 10 hid group than in the 0-5 and 6-10 h/d groups (P < 0.05-0.01), but with no statistical difference between the latter two (P > 0.05).</p><p><b>CONCLUSION</b>Computer occupation is associated with abnormal semen quality, and long-term computer use ( > 10 h/d) may be one of the factors of male infertility.</p>

Comparison of sperm parameters between male adults at different altitudes / 中华男科学杂志

<p><b>OBJECTIVE</b>To investigate the influence of long-term anoxic exposure on the sperm function of male adults at different altitudes.</p><p><b>METHODS</b>A total of 28 male adults that had stayed at the altitude of 5 340 m for 1-3 years were included as a high-altitude group (HAG), 34 at the mean altitude of 3 800 m for 2-5 years as a middle-altitude group (MAG) and 31 permanently at the altitude of 1 300 m as controls. Semen specimens were collected and the real-time semen analysis was performed by using computer-assisted semen analysis (CASA) system.</p><p><b>RESULTS</b>The sperm density, VCL, VSL, VAP and LIN in the HAG were (51.12 +/- 14.61) x 10(6)/ ml, (48.17 +/- 13. 52) microm/s, (32.64 +/- 6.70) microm/s, (41.21 +/- 9.32) microm/s and 52.24 +/- 8.14, respectively, significantly lower than those of the control (P < 0.01 or P < 0.05). Compared with the control group, there was a progressive decrease in sperm concentration, sperm motility rate, VSL, VCL, LIN, VAP and ALH in the MAG.</p><p><b>CONCLUSION</b>The higher the altitude, the more obvious was the negative effect of anoxic exposure on the sperm function of male adults.</p>

The mutant spectrum of phenylalanine hydroxylase gene in Northern Chinese / 中华医学遗传学杂志

<p><b>OBJECTIVE</b>To understand the mutant spectrum of phenylalanine hydroxylase (PAH) gene in Northern Chinese.</p><p><b>METHODS</b>All the exons and flaking introns of PAH gene were detected by PCR-single strand conformation polymorphism (PCR/SSCP) and sequencing in 230 patients with phenylketonuria (PKU).</p><p><b>RESULTS</b>(1) A total of 75 different mutations were detected in 435 out of 460 mutant alleles (94.6%). Among them 3 mutations (S251-R252>SfsX89, Y387D and A389G) have not been reported previously. The mutations, R243Q, EX6-96A>G, R111X, R413P and Y356X, were the prevalent mutations with relative frequencies of 21.7%, 10.2%, 8.3%, 6.5%, and 6.1% respectively, followed by V399V(4.1%), IVS4-1G>A (3.5%), IVS7+2T>A (2.2%) and R241C(2.2%). Most mutations were detected in exons 3, 5, 6, 7, 11 and 12 and flaking introns of PAH gene. (2) Ten polymorphism sites were detected in the study. Four sites, IVS3-22C>T, IVS10+97G>A, Q232Q and V245V, had high relative frequencies of 56.7%, 75.9%, 89.0% and 81.9% respectively. It would suggest that the race diversity exists in PAH cDNA sequence.</p><p><b>CONCLUSION</b>The mutation spectrum of PAH gene in Northern Chinese is similar to other Asian populations but significantly different from European populations.</p>

Mutations in exon 7 of the PAH gene in Chinese phenylketonuria patients in Xinjiang / 中华检验医学杂志

Objective To investigate the mutation characteristics in exon 7 of the PAH gene in phenylketonuria(PKU) patients in Xinjiang.Methods The mutations in exon 7 of PAH gene were detected by PCR/SSCP in 37 PKU patients.Results Five missense mutations including R243Q,L255S,E280G, E280K and P281L were identified in 74 chromosomes from 37 PKU patients,with relative frequencies of 18.9%,4.1%,1.4%,1.4% and 1.4% respectively.The frequency of mutant alleles in exon 7 was 27%. Among the five mutations,it was the second time the E280G mutation was reported in the world.In China,it was the second time the L255S,E280K and P281 L mutations were found.P281L and R243Q mutations were first found in 2 of Chinese Uygur.Considering the previous reports and the present study,R243Q was the most prevalent form in Asian PKU populations.P281L and E280K were two common mutations in PKU patients from European countries.However,E280G and L255S were two characteristic forms in Chinese. Condusions Characteristics of PAH gene mutations are shown in Chinese PKU population from Xinjiang, which is a special distribution belt that located between China and Europe.The results give a clue that Xinjiang could probably be an ideal genetic resource repertoire for studying diversity of gene mutations, heterogeneity of PAH gene,human genesis and migration.