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Type I R-M systems help establish the prokaryotic DNA methylation landscape and provide protection against invasive DNA. Here, the authors report on detailed structural and molecular mechanisms of a non-canonical type I R-M methyltransferase.

To better understand its mechanism of activity towards higher alcohols, we overexpressed and purified new Geotrichum candidum GDH (GcGDH). The purified GcGDH (50.27 kDa) was then crystallized, and the crystal diffracted to a resolution of 2.3 Å using X-ray diffraction. We found that the GcGDH crystal structure belonged to space group P212121 and was comprised of two hexamers organized into an asymmetric unit, with each subunit consisting of 452 amino acid residues. The binding sites between higher alcohols or L-glutamic acid and GcGDH were consistent. The optimal reaction conditions for GcGDH and hexanol were a pH of 4.0 and temperature of 30 °C, and those for GcGDH and monosodium glutamate (MSG) were a pH of 8.0 and temperature of 20 °C. The Km values for hexanol and MSG were found to be 74.78 mM and 0.018 mM, respectively. Mutating GcGDH Lys 113 to either Ala or Gly caused a dramatic reduction in its catalytic efficiency towards both MSG and hexanol, suggesting that Lys 113 is essential to the active site of GcGDH.

We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.

This study compared six models, namely the Gaines, Sikka, Nelder, Wood, Dhanoa and Hayashi models, for the estimation of 305 days milk yield in Chinese Holstein cattle. We compared their ability to reliably predict 305-day lactation yield from incomplete (3 or 6 test-day (TD)) records. Our findings revealed that the accuracies (ACC) were 0.6655–0.9948, 0.8652–0.9977 and 0.9169–0.9968, whereas the mean square errors (MSE) were 0.0121–2.4807, 0.0139–1.0716 and 0.0170–0.5528 when 3 TD records were used in the first, second and higher lactations, respectively; when 6 TD records were used, the ACC were 0.8800–0.9992, 0.8742–0.9998 and 0.7950–0.9996, whereas the MSE values were 0.0017–0.3348, 0.0011– 0.8605 and 0.0021–1.4869 in the first, second and higher lactations, respectively. All the models were fitted more accurately with 6 TD than 3 TD records. Further analysis revealed that the curves made by the Nelder, Wood and Dhanoa models were close to the actual curves. These three models can be used to predict the 305-day yield for management decisions in farms and for the genetic evaluation of Chinese Holstein cattle.

Cordyceps fumosorosea is an important species in the genus of Cordyceps, containing a variety of bioactive compounds, including fumosorinone (FU). This study was a ground-breaking assessment of FU levels in liquid and solid cultures. The present study focused on the impacts of solid-state fermentation (SSF) using solid substrates (wheat, oat, and rice), as well as the effects of fermentation parameters (pH, temperature, and incubation period), on the generation of FU. All the fermentation parameters had significant effects on the synthesis of FU. In a study of 25 °C, 5.5 pH, and 21 days of incubation period combinations calculated -to give maximal FU production, it was found that the optimal values were 25 °C, 5.5 pH, and 21 days, respectively. In a solid substrate medium culture, FU could be produced from SSF. At 30 days, a medium composed of rice yielded the most FU (798.50mg/L), followed by a medium composed of wheat and oats (640.50 and 450.50mg/L), respectively. An efficient method for increasing FU production on a large scale could be found in this approach. The results of this study might have multiple applications in different industrial fermentation processes. [ABSTRACT FROM AUTHOR]

Alternative splicing (AS) contributes to the complexity of the mammalian proteome and plays an important role in diseases, including infectious diseases. The differential AS patterns of these transcript sequences between the healthy (HS3A) and mastitic (HS8A) cows naturally infected by Staphylococcus aureus were compared to understand the molecular mechanisms underlying mastitis resistance and susceptibility. In this study, using the Illumina paired-end RNA sequencing method, 1352 differentially expressed genes (DEGs) with higher than twofold changes were found in the HS3A and HS8A mammary gland tissues. Gene ontology and KEGG pathway analyses revealed that the cytokine-cytokine receptor interaction pathway is the most significantly enriched pathway. Approximately 16k annotated unigenes were respectively identified in two libraries, based on the bovine Bos taurus UMD3.1 sequence assembly and search. A total of 52.62% and 51.24% annotated unigenes were alternatively spliced in term of exon skipping, intron retention, alternative 5' splicing and alternative 3' splicing. Additionally, 1,317 AS unigenes were HS3A-specific, whereas 1,093 AS unigenes were HS8A-specific. Some immune-related genes, such as ITGB6, MYD88, ADA, ACKR1, and TNFRSF1B, and their potential relationships with mastitis were highlighted. From Chromosome 2, 4, 6, 7, 10, 13, 14, 17, and 20, 3.66% (HS3A) and 5.4% (HS8A) novel transcripts, which harbor known quantitative trait locus associated with clinical mastitis, were identified. Many DEGs in the healthy and mastitic mammary glands are involved in immune, defense, and inflammation responses. These DEGs, which exhibit diverse and specific splicing patterns and events, can endow dairy cattle with the potential complex genetic resistance against mastitis.

[This corrects the article DOI: 10.1371/journal.pone.0159719.].

Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFI-III), and the ZHD subgroup was subdivided into five subclasses (ZHDI-V). The PsZF-HD members were named PsMIF1-PsMIF4 and PsZHD1-PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a lowtemperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas. [ABSTRACT FROM AUTHOR]

This report describes the modification of crystallization plates by simply oxidizing the surface of the protein wells. The oxidized crystallization plates were tested in standard protein crystallization screening and reproducibility studies. The results showed that the protein wells of the treated plates were smoother and more optically transparent than those of the untreated plates, and more importantly, protein crystallization was significantly promoted after the oxidation treatment. Because there is no change to the routine screening protocol, this method is simple and easy to apply in protein crystallization. [ABSTRACT FROM AUTHOR]

Heat-shock transcription factors (HSFs) play an important role in regulating heat stress response. The activation of heat-shock protein (HSP) genes is mediated by HSFs, which bind to promoters of HSP genes. In this research, two novel single nucleotide polymorphisms, T909C and G4693T, and their association with thermal tolerance were investigated in 951 Chinese Holstein cattle. Linkage disequilibrium and haplotype construction were analyzed using SHEsis software. Four haplotypes were constructed, and nine haplotype combinations were found. Potassium content in erythrocytes (PCE), decreased rate of milk production (R), rectal temperature (RT), and heat-tolerance coefficient (HTC) were selected for the thermotolerance index. Association analysis showed that thermal tolerance in Chinese Holstein cattle was significantly affected by T909C and G4693T. The PCE of cows with CC or TC genotype was lower than that of TT at the 909 position ( p < 0.05). Cows with TT genotype had lower PCE ( p < 0.01) and higher HTC ( p < 0.05) at the 4693 position. Cows with H2H4 haplotype combination had lower PCE ( p < 0.01), R ( p < 0.05) and RT ( p < 0.05) and higher HTC ( p < 0.05) than those with H1H3 haplotype combination. Bioinformatic analysis predicted that the 4693 position was located in the microRNA-binding (bta-miR-484) region. Quantitative reverse transcription-polymerase chain reaction demonstrated that 4693-T mutation caused the disruption of microRNA target binding, resulting in the relief of the transcriptional repression, which, in turn, resulted in increased expression. Thus, the HSF1 gene is useful in dairy cattle thermal tolerant breeding. [ABSTRACT FROM AUTHOR]

The cold shock domain (CSD) is an evolutionarily conserved nucleic acid binding domain that exhibits binding activity to RNA, ssDNA, and dsDNA. Mammalian CRHSP-24 contains CSD, but its structure-functional relationship has remained elusive. Here we report the crystal structure of human CRHSP-24 and characterization of the molecular trafficking of CRHSP-24 between stress granules and processing bodies in response to oxidative stress. The structure of CRHSP-24 determined by single-wavelength anomalous dispersion exhibits an a-helix and a compact β-barrel formed by five curved anti-parallel β strands. Ligand binding activity of the CSD is orchestrated by residues Ser41 to Leu43. Interestingly, a phosphomimetic S41D mutant abolishes the ssDNA binding in vitro and causes CRHSP-24 liberated from stress granules in vivo without apparent alternation of its localization to the processing bodies. This new class of phosphorylation-regulated interaction between the CSD and nucleic acids is unique in stress granule plasticity. Importantly, the association of CRHSP-24 with stress granules is blocked by PP4/PP2A inhibitor calyculin A as PP2A catalyzes the dephosphorylation of Ser41 of CRHSP-24. Therefore, we speculate that CRHSP-24 participates in oxidative stress response via a dynamic and temporal association between stress granules and processing bodies. [ABSTRACT FROM AUTHOR]

Gliding is an energetically efficient mode of locomotion that has evolved independently, and in different ways, in several tetrapod groups. Here, we report on an acrodontan lizard from the Early Cretaceous Jehol Group of China showing an array of morphological traits associated with gliding. It represents the only known occurrence of this specialization in a fossil lizard and provides evidence of an Early Cretaceous ecological diversification into an aerial niche by crown-group squamates. The lizard has a dorsal-rib-supported patagium, a structure independently evolved in the Late Triassic basal lepidosauromorph kuehneosaurs and the extant agamid lizard Draco, revealing a surprising case of convergent evolution among lepidosauromorphans. A patagial character combination of much longer bilaterally than anteroposteriorly, significantly thicker along the leading edge than along the trailing edge, tapered laterally to form a wing tip, and secondarily supported by an array of linear collagen fibers is not common in gliders and enriches our knowledge of gliding adaptations among tetrapods. [ABSTRACT FROM AUTHOR]

Pea is a conventional grain-feed-grass crop in Tibet and the only high-protein legume in the region; therefore, it plays an important role in Tibetan food and grass security. Zinc finger-homeodomain (ZF-HD) belongs to a family of homozygous heterotypic cassette genes, which play an important role in plant growth, development, and response to adversity stress. Using a bioinformatics approach, 18 PsZF-HD family members were identified. These genes were distributed across seven chromosomes and two scaffold fragments, and evolutionary analysis classified them into two subgroups, MIF and ZHD. The MIF subgroup was subdivided into three subclasses (PsMIFⅠ–III), and the ZHD subgroup was subdivided into five subclasses (ZHDⅠ–V). The PsZF-HD members were named PsMIF1–PsMIF4 and PsZHD1–PsZHD14. Twelve conserved motifs and four conserved domains were identified from PsZF-HD family, of which MIF subgroup only contained one domain, while ZHD subgroup contained two types of domains. In addition, there were significant differences in the three-dimensional structures of the protein members of the two subgroups. Most PsZF-HD genes had no introns (13/18), and only five genes had one intron. Forty-five cis-acting elements were predicted and screened, involving four categories: light response, stress, hormone, and growth and development. Transcriptome analysis of different tissues during pea growth and development showed that PsZHD11, 8, 13, 14 and MIF4 were not expressed or were individually expressed in low amounts in the tissues, while the other 13 PsZF-HDs genes were differentially expressed and showed tissue preference, as seen in aboveground reproductive organs, where PsZHD6, 2, 10 and MIF1 (except immature seeds) were highly expressed. In the aerial vegetative organs, PsZHD6, 1, and 10 were significantly overexpressed, while in the underground root system, PsMIF3 was specifically overexpressed. The leaf transcriptome under a low-nitrogen environment showed that the expression levels of 17 PsZF-HDs members were upregulated in shoot organs. The leaf transcriptome analysis under a low-temperature environment showed stress-induced upregulation of PsZHD10 and one genes and down-regulation of PsZHD6 gene. These results laid the foundation for deeper exploration of the functions of the PsZF-HD genes and also improved the reference for molecular breeding for stress resistance in peas.

Abstract This study focuses on Early Cretaceous mudstones from the Shahai and Fuxin formations in the Fuxin continental basin. We analyse chemical weathering, land surface temperatures and palaeoclimates based on chemical weathering indices, and emphasize the implications of continental chemical weathering on nutrient fluxes into lakes and oceans. According to Cr and Ni abundance, Al2O3-TiO2, La/Sc-Th/Co and V-Ni-Th×10 plots, as well as rare earth element (REE) analysis, mudstone samples from the Shahai and Fuxin formations were derived from the same type of provenance comprising mainly felsic igneous rocks. Chemical weathering trends reflected by the Chemical Index of Alteration (CIA), Weathering Index of Parker (WIP) and the Mafic Index of Alteration for Oxidative weathering environments (MIA(O)) are consistent with each other and allow the geological succession to be divided into four stages. Land surface temperatures of the Shahai and Fuxin formations are estimated based on the linear relationship of CIA to temperature, and also can be divided into four stages consistent with those determined from chemical weathering trends. During Stage A (early part of the late Aptian) chemical weathering and land surface temperatures were relatively low and showed characteristic high fluctuations, while Stage B (latest Aptian) represented a transitional period where weathering rates and temperatures increased, and high amplitude fluctuations continued. Conditions changed markedly in Stage C (early Albian) with very high and stable weathering, and warm, humid climates, while in Stage D (middle and late Albian) conditions returned to low chemical weathering and land surface temperatures. These stages of chemical weathering and land surface temperature fluctuations represent responses to global climate fluctuations during the Early Cretaceous, with the early Albian high weathering intensities and warm, humid climates combining to create high nutrient levels that would have flushed through rivers into lakes and ultimately oceans. This correlates stratigraphically with the development of Early Cretaceous black shales during Ocean Anoxic Event 1b, showing the importance of continental weathering regimes as a causal mechanism for lake and ocean anoxia.

Phosphorus (P) is an important macronutrient for plant but can also cause potential environmental risk. In this paper, we studied the long-term fertilizer experiment (started 1980) to assess the soil P dynamic, balance, critical P value and the crop yield response in Taihu Lake region, China. To avoid the effect of nitrogen (N) and potassium (K), only the following treatments were chosen for subsequent discussion, including: C0 (control treatment without any fertilizer or organic manure), CNK treatment (mineral N and K only), CNPK (balanced fertilization with mineral N, P and K), MNK (integrated organic manure and mineral N and K), and MNPK (organic manure plus balanced fertilization). The results revealed that the response of wheat yield was more sensitive than rice, and no significant differences of crop yield had been detected among MNK, CNPK and MNPK until 2013. Dynamic and balance of soil total P (TP) and Olsen-P showed soil TP pool was enlarged significantly over consistent fertilization. However, the diminishing marginal utility of soil Olsen-P was also found, indicating that high-level P application in the present condition could not increase soil Olsen-P contents anymore. Linear-linear and Mitscherlich models were used to estimate the critical value of Olsen-P for crops. The average critical P value for rice and wheat was 3.40 and 4.08 mg kg−1, respectively. The smaller critical P value than in uplands indicated a stronger ability of P supply for crops in this paddy soil. We concluded that no more mineral P should be applied in rice-wheat system in Taihu Lake region if soil Olsen-P is higher than the critical P value. The agricultural technique and management referring to activate the plant-available P pool are also considerable, such as integrated use of low-P organic manure with mineral N and K.

During cell division, interaction between kinetochores and dynamic spindle microtubules governs chromosome movements. The microtubule depolymerase mitotic centromere-associated kinesin (MCAK) is a key regulator of mitotic spindle assembly and dynamics. However, the regulatory mechanisms underlying its depolymerase activity during the cell cycle remain elusive. Here, we showed that PLK1 is a novel regulator of MCAK in mammalian cells. MCAK interacts with PLK1 in vitro and in vivo. The neck and motor domain of MCAK associates with the kinase domain of PLK1. MCAK is a novel substrate of PLK1, and the phosphorylation stimulates its microtubule depolymerization activity of MCAK in vivo. Overexpression of a polo-like kinase 1 phosphomimetic mutant MCAK causes a dramatic increase in misaligned chromosomes and in multipolar spindles in mitotic cells, whereas overexpression of a nonphosphorylatable MCAK mutant results in aberrant anaphase with sister chromatid bridges, suggesting that precise regulation of the MCAK activity by PLK1 phosphorylation is critical for proper microtubule dynamics and essential for the faithful chromosome segregation. We reasoned that dynamic regulation of MCAK phosphorylation by PLK1 is required to orchestrate faithful cell division, whereas the high levels of PLK1 and MCAK activities seen in cancer cells may account for a mechanism underlying the pathogenesis of genomic instability. [ABSTRACT FROM AUTHOR]