The incidence of surgical site infections in China

Surgical site infections (SSIs) are a common type of healthcare-associated infection. We performed a literature review to demonstrate the incidence of SSIs in mainland China based on studies since 2010. We included 231 eligible studies with ≥30 postoperative patients, comprising 14 providing overall SSI data regardless of surgical sites and 217 reporting SSIs for a specific site. We found that the overall SSI incidence was 2.91% (median; interquartile range: 1.05%, 4.57%) or 3.18% (pooled; 95% confidence interval: 1.85%, 4.51%) and the SSI incidence varied remarkably according to the surgical site between the lowest (median, 1.00%; pooled, 1.69%) in thyroid surgeries and the highest (median, 14.89%; pooled, 12.54%) in colorectal procedures. We uncovered that Enterobacterales and staphylococci were the most common types of micro-organisms associated with SSIs after various abdominal surgeries and cardiac or neurological procedures, respectively. We identified two, nine, and five studies addressing the impact of SSIs on mortality, the length of stay (LOS) in hospital, and additional healthcare-related economic burden, respectively, all of which demonstrated increased mortality, prolonged LOS, and elevated medical costs associated with SSIs among affected patients. Our findings illustrate that SSIs remain a relatively common, serious threat to patient safety in China, requiring more action. To tackle SSIs, we propose to establish a nationwide network for SSI surveillance using unified criteria with the aid of informatic techniques and to tailor and implement countermeasures based on local data and observation. We highlight that the impact of SSIs in China warrants further study.

PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants

N 6-methyladenosine (m6A), which is the mostly prevalent modification in eukaryotic mRNAs, is involved in gene expression regulation and many RNA metabolism processes. Accurate prediction of m6A modification is important for understanding its molecular mechanisms in different biological contexts. However, most existing models have limited range of application and are species-centric. Here we present PEA-m6A, a unified, modularized and parameterized framework that can streamline m6A-Seq data analysis for predicting m6A-modified regions in plant genomes. The PEA-m6A framework builds ensemble learning-based m6A prediction models with statistic-based and deep learning-driven features, achieving superior performance with an improvement of 6.7% ∼ 23.3% in the area under precision-recall curve (PRC) compared with state-of-the-art regional-scale m6A predictor WeakRM in 12 plant species. Especially, PEA-m6A is capable of leveraging knowledge from pre-trained models via transfer learning, representing an innovation in that it can improve prediction accuracy of m6A modifications under small-sample training tasks. PEA-m6A also has a strong capability for generalization, making it suitable for application in within- and cross-species m6A prediction. Overall, this study presents a promising m6A prediction tool, PEA-m6A, with outstanding performance in terms of its accuracy, flexibility, transferability and generalization ability. PEA-m6A has been packaged using Galaxy and Docker technologies for ease of use and is publicly available at https://github.com/cma2015/PEA-m6A.

Association between prepartum body condition score and prepartum and postpartum dry matter intake and energy balance in multiparous Holstein cows

The objectives of this retrospective observational study were to investigate the association between body condition score (BCS) at 21 d before calving with prepartum and postpartum dry matter intake (DMI), energy balance (EB), and milk yield. Data from 427 multigravid cows from 11 different experiments conducted at the University of Florida were used. Cows were classified according to their BCS at 21 d before calving as FAT (BCS ≥4.00; n = 83), MOD (BCS 3.25 to 3.75; n = 287), and THIN (BCS ≤3.00; n = 57). Daily DMI from -21 to -1 and from +1 to +28 DIM was individually recorded. Energy balance was calculated as the difference between net energy for lactation consumed and required. Dry matter intake in FAT cows was lesser than in MOD and THIN cows both prepartum (FAT = 9.97 ± 0.21, MOD = 11.15 ± 0.14, THIN = 11.92 ± 0.22 kg/d) and postpartum (FAT = 14.35 ± 0.49, MOD = 15.47 ± 0.38, THIN = 16.09 ± 0.47 kg/d). Dry matter intake was also lesser for MOD cows compared with THIN cows prepartum, but not postpartum. Energy balance in FAT cows was lesser than in MOD and THIN cows both prepartum (FAT = -4.16 ± 0.61, MOD = -1.20 ± 0.56, THIN = 0.88 ± 0.62 Mcal/d) and postpartum (FAT = -12.77 ± 0.50, MOD = -10.13 ± 0.29, THIN = -6.14 ± 0.51 Mcal/d). Energy balance was also lesser for MOD cows compared with THIN cows both prepartum and postpartum. There was a quadratic association between BCS at 21 d before calving and milk yield. Increasing BCS from 2.5 to 3.5 was associated with an increase in daily milk yield of 6.0 kg and 28 d cumulative milk of 147 kg. Increasing BCS from 3.5 to 4.5 was associated with a decrease in daily milk yield of 4.4 kg and 28 d cumulative milk of 116 kg. In summary, a moderated BCS at 21 d before calving was associated with intermediate DMI and EB pre- and postpartum but greater milk yield compared with thinner and fatter cows. Our findings indicate that a moderated BCS is ideal for ensuring a successful lactation.

Effects of heat stress abatement on systemic and mammary inflammation in lactating dairy cows

To examine the effects of evaporative cooling on systemic and mammary inflammation of lactating dairy cows, 30 multiparous Holstein cows (parity = 2.4, 156 d in milk) were randomly assigned to 1 of 2 treatments: cooling (CL) with fans and misters or not (NC). The experiment was divided into a 10-d baseline when all cows were cooled, followed by a 36-d environmental challenge when cooling was terminated for NC cows. The onset of environmental challenge was considered as d 1. Temperature-humidity index averaged 78.4 during the environmental challenge. Milk yield and dry matter intake (DMI) were recorded daily. Blood and milk samples were collected from a subset of cows (n = 9/treatment) on d -3, 1, 3, 7, 14, and 28 of the experiment to measure cortisol, interleukin 10 (IL10), tumor necrosis factor-α (TNF-α), haptoglobin, and lipopolysaccharide binding protein (LBP). Mammary biopsies were collected from a second subset of cows (n = 6/treatment) on d -9, 2, 10, and 36 to analyze gene expression of cytokines and haptoglobin. A subset of cows (n = 7/treatment) who were not subjected to mammary biopsy collection received a bolus of lipopolysaccharides (LPS) in the left rear quarter on d 30 of the experiment. Blood was sampled from cows and milk samples from the LPS-infused quarter were collected at -4, 0, 3, 6, 12, 24, 48, and 96 h relative to infusion, for analyses of inflammatory products. Deprivation of cooling decreased milk yield and DMI. Compared with CL cows, plasma cortisol concentration of NC cows was higher on d 1 but lower on d 28 of the experiment (cooling × time). Deprivation of cooling did not affect circulating TNF-α, IL10, haptoglobin, or LBP. Compared with CL cows, NC cows tended to have higher milk IL10 concentrations but did not show effects in TNF-α, haptoglobin, or LBP. No differences were observed in mammary tissue gene expression of TNF-α, IL10, and haptoglobin. Milk yield declined after LPS infusion but was not affected by treatment. Compared with CL cows, NC cows had greater milk somatic cell count following intramammary LPS infusion. Non-cooled cows had lower circulating TNF-α and IL10 concentrations and tended to have lower circulating haptoglobin concentrations than CL cows. Milk IL10 and TNF-⍺ concentrations were higher 3 h after LPS infusion for NC cows compared with CL cows. Additionally, NC cows tended to have higher milk haptoglobin concentration after LPS infusion than CL cows. In conclusion, deprivation of evaporative cooling had minimal effects on lactating cows' basal inflammatory status, but upregulated mammary inflammatory responses after intramammary LPS infusion.

[A dry-reagent assay to rapidly detect Mycobacterium tuberculosis using loop-mediated isothermal amplification]

A molecular diagnostic assay which could be stored at room temperature was developed to rapidly detect Mycobacterium tuberculosis (MTB) based on loop-mediated isothermal amplification (LAMP) technology and dry-reagent process. LAMP uses 4 or 6 primers and Bst DNA polymerase to amplify DNA at a constant temperature. The results showed that the LAMP assay could detect the amplification of IS6110 target gene within 20 min using real-time fluorescence signal detection. The sensitive of LAMP assay was similar to the PCR technology while the precision of PCR was better than LAMP (coefficient of variation, LAMP 18.9%, PCR 3.4%), meaning LAMP was more suitable for qualitative detection. The LAMP assay did not amplify DNA of other 10 types of pathogens, including Neisseria meningitidis, Haemophilus influenzae, Staphylococcus aureus, Streptococcus pneumoniae, Rubivirus, mumps virus, adenovirus (type 3), adenovirus (type 7), respiratory syncytial virus B and parainfluenza virus type 2, indicating a good specificity. Furthermore, a dry-reagent assay was developed using air-drying and freeze-drying process. The performance of dried reagents did not change after 10 days storage at 50 ℃, meaning the dried reagents could be stored at room temperature (25 ℃) for more than six months. The dry-reagent LAMP assay also successfully amplified MTB DNA from several clinical samples within 20 min. In conclusion, the developed LAMP assay together with isothermal amplifier could rapidly detection MTB.

Enhanced heat transfer by medical gauze for cell vitrification with French straw

BACKGROUND

Film boiling occurs in the cooling process of samples with liquid nitrogen, which limits heat transfer and decreases the cooling rate.

OBJECTIVE AND METHODS

The study developed a method to enhance convective heat transfer by wrapping the French straw (FS) with a layer of medical gauze upon cooling to eliminate film boiling. A numerical model was used to study the thermodynamic mechanism in the method.

RESULTS

Numerical simulation based on heat transfer and crystallization equations indicated that wrapping the FS with medical gauze could suppress film boiling. Experimental verification showed the increased cooling rate and better cell survival when wrapped FS was used.

CONCLUSION

Numerical simulation and experimental verification demonstrated the efficacy of wrapping FS with medical gauze for better cell cryopreservation. Doi.org/10.54680/fr23510110312.

Association of edentulism and all-cause mortality in Chinese older adults: do sex differences exist?

OBJECTIVES

Previous studies revealed that tooth loss or edentulism was related to mortality. However, research in developing countries with large numbers of elderly populations is rare, and whether sex differences exist in this relationship is unknown. This study aimed to investigate the association between edentulism and 7-year all-cause mortality among older adults in China and whether sex differences existed.

STUDY DESIGN

This was a prospective cohort study.

METHODS

Data were from 2011 to 2018 waves of the China Health and Retirement Longitudinal Study. A total of 6538 participants aged ≥60 years were included. Logistic models were adopted to estimate the risks of mortality according to edentulism.

RESULTS

The participants with edentulism at baseline were 20% more likely to die over 7 years after controlling for a set of covariates (odds ratio [OR] = 1.20, 95% confidence interval [CI]: 1.02-1.42). Moreover, edentulism was associated with a 35% higher odds of death among male participants (OR = 1.35, 95% CI: 1.08-1.70), whereas a significant association was not found in female participants.

CONCLUSIONS

The findings demonstrated that baseline edentulism predicted all-cause mortality in Chinese older adults, and sex differences existed in this association. This study implied the importance of developing oral health education programs, incorporating dietary recommendations into dental care for edentulous patients, and expanding the coverage of dental services in the health insurance system to prevent edentulism and alleviate its negative outcomes for older adults.

Genomic analyses of germline and somatic variation in high-grade serous ovarian cancer

BACKGROUND

High-grade serous ovarian cancers (HGSCs) display a high degree of complex genetic alterations. In this study, we identified germline and somatic genetic alterations in HGSC and their association with relapse-free and overall survival. Using a targeted capture of 557 genes involved in DNA damage response and PI3K/AKT/mTOR pathways, we conducted next-generation sequencing of DNA from matched blood and tumor tissue from 71 HGSC participants. In addition, we performed the OncoScan assay on tumor DNA from 61 participants to examine somatic copy number alterations (SCNA).

RESULTS

Approximately one-third of tumors had loss-of-function (LOF) germline (18/71, 25.4%) or somatic (7/71, 9.9%) variants in the DNA homologous recombination repair pathway genes BRCA1, BRCA2, CHEK2, MRE11A, BLM, and PALB2. LOF germline variants also were identified in other Fanconi anemia genes and in MAPK and PI3K/AKT/mTOR pathway genes. Most tumors harbored somatic TP53 variants (65/71, 91.5%). Using the OncoScan assay on tumor DNA from 61 participants, we identified focal homozygous deletions in BRCA1, BRCA2, MAP2K4, PTEN, RB1, SLX4, STK11, CREBBP, and NF1. In total, 38% (27/71) of HGSC patients harbored pathogenic variants in DNA homologous recombination repair genes. For patients with multiple tissues from the primary debulking or from multiple surgeries, the somatic mutations were maintained with few newly acquired point mutations suggesting that tumor evolution was not through somatic mutations. There was a significant association of LOF variants in homologous recombination repair pathway genes and high-amplitude somatic copy number alterations. Using GISTIC analysis, we identified NOTCH3, ZNF536, and PIK3R2 in these regions that were significantly associated with an increase in cancer recurrence and a reduction in overall survival.

CONCLUSIONS

From 71 patients with HGCS, we performed targeted germline and tumor sequencing and provided a comprehensive analysis of these 557 genes. We identified germline and somatic genetic alterations including somatic copy number alterations and analyzed their associations with relapse-free and overall survival. This single-site long-term follow-up study provides additional information on genetic alterations related to occurrence and outcome of HGSC. Our findings suggest that targeted treatments based on both variant and SCNA profile potentially could improve relapse-free and overall survival.

Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy

BACKGROUND

Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.

RESULTS

Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.

CONCLUSIONS

Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.

Edge-Enhancing Gradient-Echo MP2RAGE for Clinical Epilepsy Imaging at 7T

The 3D edge-enhancing gradient-echo (EDGE) MR imaging sequence offers superior contrast-to-noise ratio in the detection of focal cortical dysplasia. EDGE could benefit from 7T MR imaging but also faces challenges such as image inhomogeneity and low acquisition efficiency. We propose an EDGE-MP2RAGE sequence that can provide both EDGE and T1-weighted contrast, simultaneously, improving data-acquisition efficiency. We demonstrate that with sequence optimization, EDGE images with sufficient uniformity and T1-weighted images with high gray-to-white matter contrast can be achieved.

Hormonal and immunological responses of Holstein dairy cows from late lactation to the dry period and from the dry period to early lactation

Parturition and dry-off are challenging events for dairy cows partially due to changes in endocrine responses. The aim of this experiment was to evaluate blood concentrations of cortisol and prolactin and their effects on proliferation of peripheral blood mononuclear cells (PBMC) with or without stimulation by common immune cell mitogens (lipopolysaccharide [LPS], and concanavalin A [ConA]) of multiparous dairy cows from late lactation to the dry period and from the dry period to early lactation. Two groups of cows were enrolled: cows from late lactation to the dry period enrolled at 8 d before dry-off (LTD, n = 6, days in milk at dry-off = 332 ± 41 d) and cows from the dry period to early lactation enrolled at 7 d before expected calving date (DTL, n = 7). Blood was collected on d -8, 3, 7, and 15 relatives to dry-off for LTD cows, and on d -7, 3, 7, and 21 relatives to calving for DTL cows to analyze circulating stress hormones and to isolate PBMC. The PBMC were stimulated in vitro with prolactin (PRL), hydrocortisone (HDC), LPS, ConA, PRL + LPS, PRL + ConA, HDC+LPS, and HDC + ConA to assess proliferative responses. Plasma cortisol and PRL concentrations of LTD and DTL cows were not affected by time. Regardless of time, addition of HDC reduced PBMC proliferation stimulated by LPS, but PRL had no effect. No time effect was observed for proliferation of PBMC collected from LTD cows, but PBMC collected at 21 d after calving had higher proliferative responses to LPS and ConA than those from late dry period or early lactation. In conclusion, results from this experiment confirmed the lower PBMC proliferation during the transition period from the final week of gestation to early lactation and suggested that cows transitioning from late lactation to dry period maintained unchanged cell-mediated immune function.

Large-Scale Detection of Telomeric Motif Sequences in Genomic Data Using TelFinder

Telomeres are regions of tandem repeated sequences at the ends of linear chromosomes that protect against DNA damage and chromosome fusion. Telomeres are associated with senescence and cancers and have attracted the attention of an increasing number of researchers. However, few telomeric motif sequences are known. Given the mounting interest in telomeres, an efficient computational tool for the de novo detection of the telomeric motif sequence of new species is needed since experimental-based methods are costly in terms of time and effort. Here, we report the development of TelFinder, an easy-to-use and freely available tool for the de novo detection of telomeric motif sequences from genomic data. The vast quantity of readily available genomic data makes it possible to apply this tool to any species of interest, which will undoubtedly inspire studies requiring telomeric repeat information and improve the utilization of these genomic data sets. We have tested TelFinder on telomeric sequences available in the Telomerase Database, and the detection accuracy reaches 90%. In addition, variation analyses in telomere sequences can be performed by TelFinder for the first time. The telomere variation preference of different chromosomes and even at the ends of the chromosome can provide clues regarding the underlying mechanisms of telomeres. Overall, these results shed new light on the divergent evolution of telomeres. IMPORTANCE Telomeres are reported to be highly correlated with the cell cycle and aging. As a result, research on telomere composition and evolution has become more and more urgent. However, using experimental methods to detect telomeric motif sequences is slow and costly. To combat this challenge, we developed TelFinder, a computational tool for the de novo detection of the telomere composition only using genomic data. In this study, we showed that a lot of complicated telomeric motifs could be identified by TelFinder only using genomic data. In addition, TelFinder can be used to check variation analyses in telomere sequences, which could lead to a deeper understanding of telomere sequences.

Natural selection pressure exerted on "Silent" mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure

From the first emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) till now, multiple mutations that caused synonymous and nonsynonymous substitutions have accumulated. Among them, synonymous substitutions were regarded as "silent" mutations that received less attention than nonsynonymous substitutions that cause amino acid variations. However, the importance of synonymous substitutions can not be neglected. This research focuses on synonymous substitutions on SARS-CoV-2 and proves that synonymous substitutions were under purifying selection in its evolution. The evidence of purifying selection is provided by comparing the mutation number per site in coding and non-coding regions. We then study the two forces of purifying selection: synonymous codon usage and RNA secondary structure. Results show that the codon usage optimization leads to an adapted codon usage towards humans. Furthermore, our results show that the maintenance of RNA secondary structure causes the purifying of synonymous substitutions in the structural region. These results explain the selection pressure on synonymous substitutions during the evolution of SARS-CoV-2.

Mussel-Inspired Hydrogels for Fluoride Delivery and Caries Prevention

Fluoride agents hold promise for the repair and prevention of caries lesions, but their interaction with enamel is often hampered and diminished because of the dynamic wet environment in the oral cavity, which affects the efficacy of fluoride delivery and limits treatment success. We herein developed a mussel-inspired wet adhesive fluoride system (denoted TS@NaF) fabricated by the self-assembly of tannic acid (TA), silk fibroin (SF), and sodium fluoride (NaF). TS@NaF demonstrated remarkable biological stability and biocompatibility, showed reliable wet adhesion, released fluoride ions (F−) topically, and induced significant deposition of calcium fluoride (CaF2) onto enamel in vitro. Furthermore, TS@NaF provided an anticaries effect in vitro and induced a detectable increase in enamel mineral density. Advanced fluoride-releasing bioadhesives are therefore promising candidates for caries prevention and highlight the great potential of mussel-inspired dental materials in clinical applications.

Effect of fish oil and canola oil supplementation on immunological parameters, feed intake, and growth of Holstein calves

Supplemental n-3 fatty acids (FA) may support better immune responses than n-6 and n-9 FA in dairy calves. The objective was to evaluate the effect of n-3 FA, supplemented as a fish oil product (FO) in the milk replacer (MR), in comparison to n-6 and n-9 FA, supplemented as canola oil (CO), on body weight (BW), daily gain, and immunological parameters of preweaning Holstein calves. The study was conducted from September to December 2019. Calves were randomly allocated to a control group (n = 15; BW = 36.2 ± 1.5 kg; mean ± SEM) supplemented daily with 30 mL of CO and to an experimental group (n = 15; BW = 36.3 ± 1.5 kg) supplemented with 60 g of a product containing 30 g of FO. Both treatments were added to the MR during the morning feeding. All calves were fed 4 L of MR at 12.5% solids at 0700 and 1600 h for wk 1, 6 L from wk 2 to 7, and 3 L once daily (0700 h) during wk 8 until weaning (56 d). Blood samples were collected at 7, 14, 21, 28, 35, 42, 49, and 56 d of age for serum haptoglobin, TNF-α, IL-1β, and protectin. Dry matter intake was recorded in all experimental calves daily. Seroneutralization titers to vaccination against viral diseases (infectious bovine rhinotracheitis, parainfluenza 3, bovine viral diarrhea, and bovine respiratory syncytial virus) were determined. Mixed models for repeated measures were developed to analyze variables over time. Seroneutralization titers were analyzed by the Kruskal-Wallis test. The other variables were compared by a generalized linear model. Serum FA profile at 35 d of age showed that FO supported higher concentrations of n-3 FA than CO. Final BW [65.2 vs. 62.0 kg, standard error of the mean (SEM) = 2.1 kg] and average daily gain (0.52 vs. 0.46 kg/d, SEM = 0.1 kg/d) tended to be higher for the FO than the CO group. An interaction of treatment × day for dry matter intake was observed, especially during weaning (2.17 kg vs. 1.94 kg, SEM = 0.158 kg, for FO and CO group, respectively). Blood lactate (mmol/L) was higher in the CO than in the FO group at d 7. Haptoglobin and IL-1β were higher for the CO group on d 14 than the FO group. The TNF- α concentrations for the FO group were reduced over time, whereas the concentrations in the CO group remained constant. Protectin was higher in the FO group on d 14, but was lower on d 28, 35, and 49. Seroneutralization antibody titers postvaccination for the PI₃ virus were higher for the FO than the CO group. In conclusion, calves supplemented with FO had lower concentrations of blood lactate, haptoglobin, IL-1β and TNF-α than calves supplemented with CO during the study period. The FO supplementation had a higher DMI than CO supplementation. Results of this trial should be interpreted with caution due to the lack of a negative control group as well as the lower birth weight and growth rate observed under heat stress conditions.

A detailed comparative analysis of codon usage bias in Alongshan virus

Alongshan virus (ALSV) is an emerging tick-borne pathogen that infects humans, causing febrile disease. ALSV uses Ixodes Persulcatus ticks to infect humans with a wide range of signs, from asymptomatic to encephalitis-like syndrome. There is an increasing public health concern about the ALSV infection. To get insight into the impacts of viral relations with their hosts on viral ability, survival, and evasion from hosts immune systems remain unknown. The codon usage is a driving force in viral genome evolution; therefore, we enrolled 41 ALSV strains in codon usage analysis to elucidate the molecular evolutionary dynamics of ALSV. The results indicate that the overall codon usage among ALSV isolates is relatively similar and slightly biased. Base compositions for the cds were in order of G >A >C >U and in the third position of codons G3 >A3 >C3 >T3. The RSCU values revealed that the more frequently used codons were mostly GC ended. Different codon preferences in ALSV genes in relation to codon usage of H. sapiens and Ixodes Persulcatus genes were found. Neutrality plot was determined to reveal the superiority of natural selection over directional mutation pressure in causing CUB based on GC12 versus GC3 contents. The results of these studies suggest that the emergence of ALSV in China, Russia and Finland may also be reflected in ALSV codon usage. Altogether, the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of ALSV.

Average SAR prediction, validation, and evaluation for a compact MR scanner head-sized RF coil

A recently developed compact 3 T (C3T) MRI scanner with high performance gradients [1, 2] has a dedicated radiofrequency (RF) transmit coil that exposes only the head, neck and a small portion of the upper body region during head-first scanning. Due to the unique coil geometry and patient positioning, the established SAR model used for a conventional whole-body scanner cannot be directly translated to the C3T. Here a specific absorption rate (SAR) estimation and validation framework was developed and used to implement a dedicated and accurate SAR prediction model for the C3T. Two different SAR prediction models for the C3T were defined and evaluated: one based on an anatomically derived exposed mass, and one using a fixed anatomical position located caudally to the RF coil to determine the exposed mass. After coil modeling and virtual human body simulation, the designed SAR prediction model was implemented on the C3T and verified with calorimetry and in vivo scan power monitoring. The fixed-demarcation exposed mass model was selected as appropriate exposed mass region to accurately estimate the SAR deposition in the patient on the C3T.

Genome-wide characterization, evolution, structure, and expression analysis of the F-box genes in Caenorhabditis

BACKGROUND

F-box proteins represent a diverse class of adaptor proteins of the ubiquitin-proteasome system (UPS) that play critical roles in the cell cycle, signal transduction, and immune response by removing or modifying cellular regulators. Among closely related organisms of the Caenorhabditis genus, remarkable divergence in F-box gene copy numbers was caused by sizeable species-specific expansion and contraction. Although F-box gene number expansion plays a vital role in shaping genomic diversity, little is known about molecular evolutionary mechanisms responsible for substantial differences in gene number of F-box genes and their functional diversification in Caenorhabditis. Here, we performed a comprehensive evolution and underlying mechanism analysis of F-box genes in five species of Caenorhabditis genus, including C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei.

RESULTS

Herein, we identified and characterized 594, 192, 377, 39, 1426 F-box homologs encoding putative F-box proteins in the genome of C. brenneri, C. briggsae, C. elegans, C. japonica, and C. remanei, respectively. Our work suggested that extensive species-specific tandem duplication followed by a small amount of gene loss was the primary mechanism responsible for F-box gene number divergence in Caenorhabditis genus. After F-box gene duplication events occurred, multiple mechanisms have contributed to gene structure divergence, including exon/intron gain/loss, exonization/pseudoexonization, exon/intron boundaries alteration, exon splits, and intron elongation by tandem repeats. Based on high-throughput RNA sequencing data analysis, we proposed that F-box gene functions have diversified by sub-functionalization through highly divergent stage-specific expression patterns in Caenorhabditis species.

CONCLUSIONS

Massive species-specific tandem duplications and occasional gene loss drove the rapid evolution of the F-box gene family in Caenorhabditis, leading to complex gene structural variation and diversified functions affecting growth and development within and among Caenorhabditis species. In summary, our findings outline the evolution of F-box genes in the Caenorhabditis genome and lay the foundation for future functional studies.

Maternal heat stress reduces body and organ growth in calves: Relationship to immune status

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In utero heat stress reduces growth relative to calves born to cooled dams.

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Immune organ growth is further compromised beyond whole body growth.

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Jejunal enterocyte apoptosis is accelerated at birth after in utero heat stress.

Late-gestation heat stress of dairy cows reduces fetal growth and influences postnatal performance and immune status of the offspring. Our first objective was to evaluate the effect of in utero heat stress on overall fetal and organ growth, particularly organs associated with immune function. The second objective was to examine the cellular mechanism of altered passive immunity in neonatal bull calves after in utero heat stress. Specifically, we examined the rate of apoptosis of intestinal cells early in life, as it is associated with gut closure. Dams were dried off approximately 45 d before expected calving and randomly assigned to 1 of 2 treatments: heat stress (HT) or cooling (CL). During the dry period all cows were housed under shade in a freestall barn, where the pen for CL cows was equipped with active cooling, including water soakers and fans, whereas the pen for HT cows had no soakers or fans. Using rectal temperature and respiration rate as indicators, heat stress was severe. Average rectal temperature in HT cows was 39.3°C compared with 39.0°C in CL cows, and HT cows had a respiration rate of 66.7 breaths/min compared with 43.2 breaths/min for CL cows. Bull calves (n = 30) were immediately separated from their dams at birth, weighed, and then killed before colostrum feeding (n = 5/treatment; d 0) or at 1 or 2 d of age following colostrum feeding (n = 5/treatment per day). After slaughter, the small intestine was removed and weighed, and samples from the jejunum were fixed for immunohistochemistry. Birth weight of bulls from HT dams was 1.1 kg lower than that of bulls from CL dams. Thymus, spleen, and heart weights of HT bulls were lower relative to those of CL bulls, whereas liver weight of HT bulls tended to be lower relative to that of CL bulls. Jejunal cell apoptosis decreased with age in both HT and CL calves after birth, mirroring gut closure. However, in utero heat stress increased the apoptotic rate in the jejunum, particularly at birth. We conclude that the chronic exposure to heat strain of HT compared with CL dams in late gestation significantly affected fetal growth and immune tissue development, which may be associated with reduced immune function in early life. Also, late-gestation heat stress increased calves' intestinal apoptosis in the first 2 d of life, which might explain the decreased IgG uptake and limited passive immune competence observed in previous studies.

Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus

The molecular evolutionary dynamics that shape hantaviruses’ evolution are poorly understood even now, besides the contribution of virus-host interaction to their evolution remains an open question. Our study aimed to investigate these two aspects in Hantaan virus (HTNV)—the prototype of hantaviruses and an emerging zoonotic pathogen that infects humans, causing hemorrhagic fever with renal syndrome (HFRS): endemic in Far East Russia, China, and South Korea—via a comprehensive, phylogenetic-dependent codon usage analysis. We found that host- and natural reservoir-induced natural selection is the primary determinant of its biased codon choices, exceeding the mutational bias effect. The phylogenetic analysis of HTNV strains resulted in three distinct clades: South Korean, Russian, and Chinese. An effective number of codon (ENC) analysis showed a slightly biased codon usage in HTNV genomes. Nucleotide composition and RSCU analyses revealed a significant bias toward A/U nucleotides and A/U-ended codons, indicating the potential influence of mutational bias on the codon usage patterns of HTNV. Via ENC-plot, Parity Rule 2 (PR2), and neutrality plot analyses, we would conclude the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of HTNV; however, natural selection is the dominant factor influencing its codon usage bias. Codon adaptation index (CAI), Relative codon deoptimization index (RCDI), and Similarity Index (SiD) analyses uncovered the intense selection pressure from the host (Human) and natural reservoirs (Striped field mouse and Chinese white-bellied rat) in shaping HTNV biased codon choices. Our study clearly revealed the evolutionary processes in HTNV and the role of virus-host interaction in its evolution. Moreover, it opens the door for a more comprehensive codon usage analysis for all hantaviruses species to determine their molecular evolutionary dynamics and adaptability to several hosts and environments. We believe that our research will help in a better and deep understanding of HTNV evolution that will serve its future basic research and aid live attenuated vaccines design.

Altered Metabolic Strategies: Elaborate Mechanisms Adopted by Oenococcus oeni in Response to Acid Stress

Oenococcus oeni plays a key role in inducing malolactic fermentation in wine. Acid stress is often encountered under wine conditions. However, the lack of systematic studies of acid resistance mechanisms limits the downstream fermentation applications. In this study, the acid responses of O. oeni were investigated by combining transcriptome, metabolome, and genome-scale metabolic modeling approaches. Metabolite profiling highlighted the decreased abundance of nucleotides under acid stress. The gene-metabolite bipartite network showed negative correlations between nucleotides and genes involved in ribosome assembly, translation, and post-translational processes, suggesting that stringent response could be activated under acid stress. Genome-scale metabolic modeling revealed marked flux rerouting, including reallocation of pyruvate, attenuation of glycolysis, utilization of carbon sources other than glucose, and enhancement of nucleotide salvage and the arginine deiminase pathway. This study provided novel insights into the acid responses of O. oeni, which will be useful for designing strategies to address acid stress in wine malolactic fermentation.

Analysis of codon usage patterns and influencing factors in rice tungro bacilliform virus

Rice tungro bacilliform virus (RTBV) belongs to genus Tungrovirus within the family Caulimoviridae harbors circular double-stranded DNA (dsDNA). Rice tungro disease (RTD) caused by RTBV, responsible for severe rice yield losses in South and Southeast Asia. Here, we performed a systematic evolutionary and codon usage bias (CUB) analysis of RTBV genome sequences. We analysed different bioinformatics techniques to calculate the nucleotide compositions, the relative synonymous codon usage (RSCU), and other indices. The results indicated slightly or low codon usage bias in RTBV isolates. Mutation and natural selection pressures have equally contributed to this low codon usage bias. Additionally, multiple factors such as host, geographical distribution also affect codon usage patterns in RTBV genomes. RSCU analysis revealed that RTBV shows mutation bias and prefers A and U ended codons to code amino acids. Codon usage patterns of RTBV were also found to be influenced by its host. This indicates that RTBV have evolved codon usage patterns that are specific to its host. The findings from this study are expected to increase our understanding of factors leading to viral evolution and fitness with respect to hosts and the environment.

Effects of evaporative cooling and dietary zinc source on heat shock responses and mammary gland development in lactating dairy cows during summer

The objective of this study was to examine the effects of evaporative cooling and dietary supplemental Zn source on heat shock responses and mammary gland development of lactating dairy cows during summer. Seventy-two multiparous lactating Holstein cows were randomly assigned to 1 of 4 treatments in a 2 × 2 factorial arrangement. Cows were either cooled (CL) or not cooled (NC) and fed diets supplemented with 75 mg of Zn/kg of dry matter (DM) from Zn hydroxychloride (IOZ) or 35 mg of Zn/kg of DM from Zn hydroxychloride plus 40 mg of Zn/kg of DM from Zn-Met complex (ZMC). The 168-d trial included a 12-wk baseline phase when all cows were cooled and fed respective dietary treatments, and a subsequent 12-wk environmental challenge phase when NC cows were deprived of evaporative cooling. Plasma was collected from a subset of cows (n = 24) at 1, 3, 5, 12, 26, 41, 54, 68, 81 d of the environmental challenge to measure heat shock protein (HSP) 70 concentration. Mammary biopsies were collected from another subset of cows (n = 30) at enrollment (baseline samples) and at d 7 and 56 of the environmental challenge to analyze gene expression related to heat shock response, apoptosis and anti-oxidative enzymes, and to examine apoptosis and cell proliferation using immunohistochemistry. Supplemental Zn source did not affect milk yield but NC cows produced less milk than CL cows. Supplemental Zn source had no effect on mammary gene expression of HSP27, 70, and 90 or plasma concentrations of HSP70. The NC cows had greater mammary gene expression of HSP than CL cows. Circulating HSP70 of NC cows gradually increased and was higher at 81 d of environmental challenge compared with CL cows. Relative to IOZ, ZMC cows tended to have lower total mammary cell proliferation but greater mammary apoptosis. There was a tendency of greater TNFRSF1A mRNA expression for ZMC compared with IOZ cows, which may suggest upregulated extrinsic apoptosis. At d 7 of environmental challenge, NC cows had numerically higher mammary apoptosis than CL cows although not statistically significant. The NC cows tended to have greater mRNA expression of CAT and SOD3 regardless of time, and had greater mRNA expression of GPX1 at d 56 and FAS at d 7 of the environmental challenge than CL cows. Relative to CL cows, mammary cell proliferation rate was higher for NC cows at d 56 of the environmental challenge. In conclusion, dietary source of supplemental Zn has substantial effect on mammary cell turnover in lactating dairy cows, and prolonged exposure to heat stress increases mammary cell proliferation.

The effect of in-hospital high-dose vs. low-dose intensive statin in patients with non-ST segment elevation acute coronary syndrome

Background

Statins remain a standard treatment for acute coronary syndrome (ACS) patients. We aimed to determine the association between different dosages of in-hospital statins and the prognoses among patients receiving percutaneous coronary intervention (PCI).

Methods

NSTE-ACS patients were retrospectively enrolled from January 2010 to December 2014 from five centres in China. Patients receiving either atorvastatin or rosuvastatin during their hospitalizations were included. All the patients were categorized into high-dose statin group (40mg atorvastatin or 20mg rosuvastatin) or low-dose statin group (20mg atorvastatin or 10mg rosuvastatin). In-hospital events and long-term all-cause death was recorded.

Results

Of the 7,008 patients included in the study, 5,248 received low-dose intensive statin (mean age: 64.28±10.39; female: 25.2%), and 1,760 received high-dose intensive statin (mean age: 63.68±10.59; female: 23.1%). There was no significant difference in in-hospital all-cause death between the two groups (adjusted OR, 1.27; P=0.665). All-cause death was similar between the two groups during the long-term follow-up period (30-day: adjusted HR, 1.28; P=0.571; 3-year: adjusted HR, 0.83; P=0.082). However, there was a robust association between the high-dose statin and the reduction in in-hospital dialysis (adjusted OR, 0.11; P=0.030).

Conclusions

The in-hospital high-dose intensive statin is not associated with lower risks of in-hospital or follow-up all-cause death in NSTE-ACS patients undergoing PCI. Considering the robust beneficial effect of in-hospital dialysis, an individualized high-dose intensive statin can be rational in specified populations.

Univariate and multivariate analyses

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): The Science and Technology Planning Project of Guangzhou City athe China Youth Research Funding

Origin and Evolution of Fusidane-Type Antibiotics Biosynthetic Pathway through Multiple Horizontal Gene Transfers

Fusidane-type antibiotics represented by fusidic acid, helvolic acid, and cephalosporin P1 have very similar core structures, but they are produced by fungi belonging to different taxonomic groups. The origin and evolution of fusidane-type antibiotics biosynthetic gene clusters (BGCs) in different antibiotics producing strains remained an enigma. In this study, we investigated the distribution and evolution of the fusidane BGCs in 1,284 fungal genomes. We identified 12 helvolic acid BGCs, 4 fusidic acid BGCs, and 1 cephalosporin P1 BGC in Pezizomycotina fungi. Phylogenetic analyses indicated six horizontal gene transfer (HGT) events in the evolutionary trajectory of the BGCs, including 1) three transfers across Eurotiomycetes and Sordariomycetes classes; 2) one transfer between genera under Sordariomycetes class; and 3) two transfers within Aspergillus genus under Eurotiomycetes classes. Finally, we proposed that the ancestor of fusidane BGCs would be originated from the Zoopagomycota by ancient HGT events according to the phylogenetic trees of key enzymes in fusidane BGCs (OSC and P450 genes). Our results extensively clarify the evolutionary trajectory of fusidane BGCs by HGT among distantly related fungi and provide new insights into the evolutionary mechanisms of metabolic pathways in fungi.

When do dry cows get heat stressed? Correlations of rectal temperature, respiration rate, and performance

Previous studies have documented the negative effects of heat stress during the dry period on dairy cow performance during the next lactation, but an easy method to assess heat stress for dry cow management is lacking. In an effort to determine a threshold for heat stress based on the physiological response of respiration rate, an easily measured variable, an analysis including data collected from 6 different studies (n = 144 cows) was performed to summarize the correlations among rectal temperature (RT) and respiration rate (RR) during the dry period, milk production during the first 8 wk of lactation (MK), calf birth weight (CW), body weight at calving (BW), gestation length (GL), and dry matter intake (DMI) pre- and postpartum. Studies were conducted in Florida during the summer, and dry cows were assigned to 2 treatments: heat stress (only shade; HT, n = 75 cows) and cooling (shade, fans, and soakers; CL, n = 69 cows). Average RT (0.3°C) and RR [26 breaths per min (bpm)] of HT cows increased compared with CL. In addition, the CL group produced more milk (2.8 kg/d) during the first 8 wk of the subsequent lactation relative to HT. Correlation analysis indicated that RR of HT was negatively correlated with MK and GL. Within HT, RT was also negatively correlated with MK and GL and tended to be negatively correlated with CW. In addition to being negatively correlated with RT and RR, HT MK was positively correlated with CW, GL, and DMI postpartum. In CL, no correlations were observed for RR, but RT was positively correlated with BW, and MK was positively correlated with DMI postpartum and tended to be positively correlated with GL. Moreover, the overall RT was 39.1 ± 0.48°C and RR was 61 ± 19.5 bpm, which indicates that RR over 61 bpm is an indicator of heat stress in cows during the dry period and can be easily assessed at the cow level. In summary, the more heat load a cow carries in the dry period, the greater the negative effects are on subsequent milk production, which may suggest a threshold for the effects of heat stress. Also, variation among cows within the HT group indicates that cows with longer gestation length have heavier calves, eat more postpartum, and produce more milk, but not as much as CL cows.

Codon Usage Bias Analysis of Bluetongue Virus Causing Livestock Infection

Bluetongue virus (BTV) is a double-stranded RNA virus with multiple segments and belongs to the genus Orbivirus within the family Reoviridae. BTV is spread to livestock through its dominant vector, biting midges of genus Culicoides. Although great progress has been made in genomic analyses, it is not fully understood how BTVs adapt to their hosts and evade the host's immune systems. In this study, we retrieved BTV genome sequences from the National Center for Biotechnology Information (NCBI) database and performed a comprehensive research to explore the codon usage patterns in 50 BTV strains. We used bioinformatic approaches to calculate the relative synonymous codon usage (RSCU), codon adaptation index (CAI), effective number of codons (ENC), and other indices. The results indicated that most of the overpreferred codons had A-endings, which revealed that mutational pressure was the major force shaping codon usage patterns in BTV. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Based on the RSCU values, we performed a comparative analysis between BTVs and their hosts, suggesting that BTVs were inclined to evolve their codon usage patterns that were comparable to those of their hosts. Such findings will be conducive to understanding the elements that contribute to viral evolution and adaptation to hosts.

RSVdb: a comprehensive database of transcriptome RNA structure

RNA fulfills a crucial regulatory role in cells by folding into a complex RNA structure. To date, a chemical compound, dimethyl sulfate (DMS), has been developed to probe the RNA structure at the transcriptome level effectively. We proposed a database, RSVdb (https://taolab.nwafu.edu.cn/rsvdb/), for the browsing and visualization of transcriptome RNA structures. RSVdb, including 626 225 RNAs with validated DMS reactivity from 178 samples in eight species, supports four main functions: information retrieval, research overview, structure prediction and resource download. Users can search for species, studies, transcripts and genes of interest; browse the quality control of sequencing data and statistical charts of RNA structure information; preview and perform online prediction of RNA structures in silico and under DMS restraint of different experimental treatments and download RNA structure data for species and studies. Together, RSVdb provides a reference for RNA structure and will support future research on the function of RNA structure at the transcriptome level.

The role of macrophages during breast cancer development and response to chemotherapy

Macrophages play an important role in the immune system as a key host defense against pathogens. Non-polarized macrophages can differentiate into pro-inflammatory classical pathway-activated macrophages or anti-inflammatory alternative pathway-activated macrophages, both of which play central roles in breast cancer growth and progression in a process called polarization of macrophages. Classical pathway-activated and alternative pathway-activated macrophages can transform into each other and their transformational properties and orientation are determined by cytokines in the tumor microenvironment. Tumor-associated macrophages display many functions, such as tissue reforming, participating in inflammation and tumor growth in breast cancer progression. Some cytokines, such as interleukins and transcriptional activators, reside in the tumor microenvironment and influence tumor-associated macrophages. Chemotherapy is a common treatment for breast cancer and macrophages play an important role in mammary tumor cell migration, cancer invasion, and angiogenesis. This review summarizes the activities of tumor-associated macrophages in the mammary tumor, chemotherapeutic processes and some potential strategies for breast cancer therapy.

Symposium review: One-carbon metabolism and methyl donor nutrition in the dairy cow

The present review focuses on methyl donor metabolism and nutrition in the periparturient and lactating dairy cow. Methyl donors are involved in one-carbon metabolism, which includes the folate and Met cycles. These cycles work in unison to support lipid, nucleotide, and protein synthesis, as well as methylation reactions and the maintenance of redox status. A key feature of one-carbon metabolism is the multi-step conversion of tetrahydrofolate to 5-methyltetrahyrofolate. Homocysteine and 5-methyltetrahyrofolate are utilized by vitamin B₁₂-dependent Met synthase to couple the folate and Met cycles and generate Met. Methionine may also be remethylated from choline-derived betaine under the action of betaine hydroxymethyltransferase. Regardless, Met is converted within the Met cycle to S-adenosylmethionine, which is universally utilized in methyl-group transfer reactions including the synthesis of phosphatidylcholine. Homocysteine may also enter the transsulfuration pathway to generate glutathione or taurine for scavenging of reactive oxygen metabolites. In the transition cow, a high demand exists for compounds with a labile methyl group. Limited methyl group supply may contribute to inadequate hepatic phosphatidylcholine synthesis and hepatic triglyceride export, systemic oxidative stress, and compromised milk production. To minimize the perils associated with methyl donor deficiency, the peripartum cow relies on de novo methylneogenesis from tetrahydrofolate. In addition, dietary supplementation of rumen-protected folic acid, vitamin B₁₂, Met, choline, and betaine are potential nutritional approaches to target one-carbon pools and improve methyl donor balance in transition cows. Such strategies have merit considering research demonstrating their ability to improve milk production efficiency, milk protein synthesis, hepatic health, and immune response. This review aims to summarize the current understanding of folic acid, vitamin B₁₂, Met, choline, and betaine utilization in the dairy cow. Methyl donor co-supplementation, fatty acid feeding strategies that may optimize methyl donor supplementation efficacy, and potential epigenetic mechanisms are also considered.

Implication of the gut microbiome composition of type 2 diabetic patients from northern China

Emerging evidence has suggested the association of the gut microbiome with some human diseases, including type 2 diabetes (T2D). In this study, we analyzed the gut microbiota from a cohort of healthy and diabetic Chinese individuals from Northern China. Pyrosequencing of the V4V5 region of 16S rRNA genes revealed a significant decrease in the gut microbiota diversity of diabetic patients as compared to healthy individuals. Butyrate-producing bacteria such as Bifidobacterium and Akkermansia were significantly decreased in diabetic patients. Furthermore, the abundance of Dorea was significantly increased in T2D individuals and negatively correlated with the abundance of butyrate-producing bacteria. The increase of Dorea could play a role in the development of T2D and has been previously overlooked. Importantly, functional analysis of the gut microbiome revealed for the first time that increased levels of butyrate production via transferases and the degradation of several amino acids due to gut microbial metabolism have strong correlations with T2D in Northern China. Moreover, the potential of gut microbiota-based classifiers to identify individuals with a high risk for T2D has been demonstrated in this study. Taken together, our findings have revealed a previously unappreciated association of the gut microbiome with T2D and have also suggested that changes in gut microbiota may be used to identify individuals at high risk for T2D.

Genomic insight into the origins and evolution of symbiosis genes in Phaseolus vulgaris microsymbionts

Background

Phaseolus vulgaris (common bean) microsymbionts belonging to the bacterial genera Rhizobium, Bradyrhizobium, and Ensifer (Sinorhizobium) have been isolated across the globe. Individual symbiosis genes (e.g., nodC) of these rhizobia can be different within each genus and among distinct genera. Little information is available about the symbiotic structure of indigenous Rhizobium strains nodulating introduced bean plants or the emergence of a symbiotic ability to associate with bean plants in Bradyrhizobium and Ensifer strains. Here, we sequenced the genomes of 29 representative bean microsymbionts (21 Rhizobium, four Ensifer, and four Bradyrhizobium) and compared them with closely related reference strains to estimate the origins of symbiosis genes among these Chinese bean microsymbionts.

Results

Comparative genomics demonstrated horizontal gene transfer exclusively at the plasmid level, leading to expanded diversity of bean-nodulating Rhizobium strains. Analysis of vertically transferred genes uncovered 191 (out of the 2654) single-copy core genes with phylogenies strictly consistent with the taxonomic status of bacterial species, but none were found on symbiosis plasmids. A common symbiotic region was wholly conserved within the Rhizobium genus yet different from those of the other two genera. A single strain of Ensifer and two Bradyrhizobium strains shared similar gene content with soybean microsymbionts in both chromosomes and symbiotic regions.

Conclusions

The 19 native bean Rhizobium microsymbionts were assigned to four defined species and six putative novel species. The symbiosis genes of R. phaseoli, R. sophoriradicis, and R. esperanzae strains that originated from Mexican bean-nodulating strains were possibly introduced alongside bean seeds. R. anhuiense strains displayed distinct host ranges, indicating transition into bean microsymbionts. Among the six putative novel species exclusive to China, horizontal transfer of symbiosis genes suggested symbiosis with other indigenous legumes and loss of originally symbiotic regions or non-symbionts before the introduction of common bean into China. Genome data for Ensifer and Bradyrhizobium strains indicated symbiotic compatibility between microsymbionts of common bean and other hosts such as soybean.

Pre- and postnatal heat stress abatement affects dairy calf thermoregulation and performance

Prenatal heat stress during late gestation exerts long-term effects on growth and productivity of the dairy calf. Further, direct exposure to heat stress during the preweaning period impairs calf thermoregulation and performance. We examined the effects of heat stress abatement during the prenatal period, postnatal period, or both on calf performance. We hypothesized that calves exposed to pre- and postnatal heat stress abatement would perform most optimally in terms of thermoregulation, growth, and health responses when compared with calves that are heat-stressed at any time in the pre- or postnatal periods. Holstein calves born to heat-stressed (HT) or cooled (CL) dams during late gestation (44 ± 5 d; prenatal HT or CL) were exposed to heat stress or cooling postnatally for 56 d (postnatal HT or CL), resulting in 4 treatments: HT-HT, HT-CL, CL-HT, and CL-CL; n = 12/treatment. Calves were administered 4 L of pooled colostrum and after 2 d of age allotted 10 L/d milk replacer and up to 3 kg/d concentrate in automatic feeder group pens (n = 6/pen). Postnatal cooling was achieved by 2 fans (average wind speed 2 m/s). Thermoregulatory responses (respiration rate and heart rate; rectal, body, and skin temperature), feed intake, growth parameters including average daily gain and medication events were recorded, and blood samples were collected weekly. Thermoregulatory responses were lower in postnatal CL calves compared with postnatal HT. In the afternoon, HT-HT calves had the highest respiration rate and rectal temperature, HT-CL calves had the lowest respiration rate, and CL-HT calves had the lowest heart rate compared with the other treatment groups. Prenatal CL calves weighed more at birth and weaning with a tendency for greater average daily gain compared with prenatal HT calves, whereas postnatal CL calves had increased milk replacer and concentrate intake and a tendency for reduced fever, infection, and total medication events relative to postnatal HT. Prenatal HT calves were esophageal tube fed more often than prenatal CL. Blood hematocrit and 24-h serum IgG concentration were greater in prenatal CL calves relative to prenatal HT. Prenatal heat stress abatement improves weight gain, hematocrit, and immunoglobulin transfer, whereas postnatal heat stress abatement modulates thermoregulatory responses, feed intake, and calf health. This study is the first to characterize the combined effects of pre- and postnatal heat stress or active cooling on the dairy calf.

Effects of milk replacer feeding levels on performance and metabolism of preweaned dairy calves during summer

The objective of this study was to evaluate the effect of milk replacer (MR) feeding programs on performance and metabolism during summer. At 3 d of age (DOA), calves were randomly assigned to 1 of 4 dietary treatments: control [CON; 0.55 kg dry matter (DM) of a 20% crude protein (CP) and 20% fat MR per day], intermediate (IL; 0.66 kg DM of a 26% CP and 17% fat MR per day), high (HL; 0.77 kg DM of a 26% CP and 17% fat MR per day), or aggressive (AL; 0.87 kg DM of a 26% CP and 17% fat MR per day). Calves were managed similarly and housed in individual polyethylene hutches using sand as a bedding material. Because 3 calves fed the AL diet developed abomasum bloating during the first 30 DOA, the AL treatment was terminated. Milk replacer (12.5% solids) was offered twice daily until 42 DOA, when MR was fed once daily to reduce its intake by 50%. Calves were weaned at 49 DOA and remained in hutches until 56 DOA. Calf starter and water were offered ad libitum. Ambient temperature and relative humidity in and outside the hutches were assessed hourly. Starter and MR intakes were recorded daily. Respiration rate and rectal temperature were determined 3 times each week. Body weight was measured at 3, 14, 28, 42, and 56 DOA. Plasma was collected at 5, 10, 14, 28, 42, 43, 45, 47, 49, 51, and 56 DOA for analysis of glucose, β-hydroxybutyrate, triglycerides, nonesterified fatty acids, urea nitrogen, and insulin concentrations. There were no treatment effects on starter intake, rectal temperature, or respiration rate. By 7 DOA, calves fed the IL and HL diets consumed the same amount of MR and a higher amount of MR than the CON calves. At wk 2, calves from all treatments had similar MR consumption before returning to the projected intake by design at wk 4. Calves fed the IL and HL treatments had similar body weight but were heavier than those fed the CON diet at wk 6, 7, and 8. Calves fed the IL and HL diets had similar average daily gain, which was higher than that of calves fed the CON diet. There was no difference in plasma metabolites among treatments, but insulin concentration increased as milk allowance increased. In summary, feeding an intermediate level of MR during summer improved calf growth compared with the CON diet, but a higher MR allowance did not support further improvements in calf performance.

Exploring the evolutionary dynamics of Rhizobium plasmids through bipartite network analysis

The genus Rhizobium usually has a multipartite genome architecture with a chromosome and several plasmids, making these bacteria a perfect candidate for plasmid biology studies. As there are no universally shared genes among typical plasmids, network analyses can complement traditional phylogenetics in a broad-scale study of plasmid evolution. Here, we present an exhaustive analysis of 216 plasmids from 49 complete genomes of Rhizobium by constructing a bipartite network that consists of two classes of nodes, the plasmids and homologous protein families that connect them. Dissection of the network using a hierarchical clustering strategy reveals extensive variety, with 34 homologous plasmid clusters. Four large clusters including one cluster of symbiotic plasmids and two clusters of chromids carrying some truly essential genes are widely distributed among Rhizobium. In contrast, the other clusters are quite small and rare. Symbiotic clusters and rare accessory clusters are exogenetic and do not appear to have co-evolved with the common accessory clusters; the latter ones have a large coding potential and functional complementarity for different lifestyles in Rhizobium. The bipartite network also provides preliminary evidence of Rhizobium plasmid variation and formation including genetic exchange, plasmid fusion and fission, exogenetic plasmid transfer, host plant selection, and environmental adaptation.

Association of dry matter intake and energy balance prepartum and postpartum with health disorders postpartum: Part II. Ketosis and clinical mastitis

The main objective of this study was to determine the association of dry matter intake as percentage of body weight (DMI%BW) and energy balance (EB) prepartum (-21 d relative to parturition) and postpartum (28 d) with ketosis (n = 189) and clinical mastitis (n = 79). For this, DMI%BW and EB were the independent variables and ketosis and clinical mastitis were the dependent variables. A secondary objective was to evaluate prepartum DMI%BW and EB as predictors of ketosis and clinical mastitis. For this, ketosis and clinical mastitis were the independent variables and DMI%BW and EB were the dependent variables. Data from 476 cows from 9 experiments were compiled. Clinical mastitis was diagnosed if milk from 1 or more quarters was abnormal in color, viscosity, or consistency, with or without accompanying heat, pain, redness, or swelling of the quarter or generalized illness, during the first 28 d postpartum. Ketosis was defined as the presence of acetoacetate in urine that resulted in any color change [5 mg/dL (trace) or higher] in the urine test strip (Ketostix, Bayer, Leverkusen, Germany). Cows that developed ketosis had lesser DMI%BW and lesser EB on d -5, -3, -2, and -1 than cows without ketosis. Each 0.1-percentage point decrease in the average DMI%BW and each 1-Mcal decrease in the average of EB in the last 3 d prepartum increased the odds of having ketosis by 8 and 5%, respectively. Cut-offs for DMI%BW and EB during the last 3 d prepartum to predict ketosis were established and were ≤1.5%/d and ≤1.1 Mcal/d, respectively. Cows that developed ketosis had lesser postpartum DMI%BW and EB and greater energy-corrected milk (ECM) than cows without ketosis. Cows that developed clinical mastitis had lesser DMI%BW but similar prepartum EB compared with cows without clinical mastitis. Each 0.1-percentage point decrease in the average DMI%BW and each 1-Mcal decrease in the average EB in the last 3 d prepartum increased the odds of having clinical mastitis by 10 and 8%, respectively. The average DMI%BW and EB during the last 3 d prepartum produced significant cut-offs to predict clinical mastitis postpartum, which were ≤1.2%/d and ≤1.0 Mcal/d, respectively. Cows that developed clinical mastitis had lesser postpartum DMI%BW from d 3 to 15 and on d 17; greater EB on d 18, from d 21 to 23, and on d 26; and lesser ECM. The main limitation in this study is that the time-order of disease relative to DMI%BW and ECM is inconsistent such that postpartum outcomes were measured before and after disease, which was diagnosed at variable intervals after calving. In summary, measures of prepartum DMI were associated with and were predictors of ketosis and clinical mastitis postpartum, although the effect sizes were small.

Association of dry matter intake and energy balance prepartum and postpartum with health disorders postpartum: Part I. Calving disorders and metritis

The main objective of this study was to determine the association of dry matter intake as percentage of body weight (DMI%BW) and energy balance (EB) prepartum (-21 d relative to parturition) and postpartum (28 d) with calving disorders (CDZ; dystocia, twins, and stillbirths; n = 101) and metritis (n = 114). For this, DMI%BW and EB were the independent variables and CDZ and metritis were the dependent variables. A secondary objective was to evaluate prepartum DMI%BW and EB as predictors of CDZ and metritis. For this, CDZ and metritis were the independent variables and DMI%BW and EB were the dependent variables. Data from 476 cows from 9 experiments were compiled. Cows that developed CDZ had lesser postpartum DMI%BW from d 3 to 12 and lesser energy-corrected milk (ECM) than cows that did not develop CDZ. Dry matter intake as percentage of BW and EB prepartum did not affect the odds of CDZ. Cows with metritis had lesser prepartum DMI%BW and EB. Each 0.1-percentage point decrease in the average DMI%BW and each 1-Mcal decrease in the average EB in the last 3 d prepartum increased the odds of having metritis by 8%. The average DMI%BW and EB during the last 3 d prepartum produced significant cut-offs to predict metritis postpartum, which were ≤1.6%/d and ≤2.5 Mcal/d, respectively. Cows that developed metritis had lesser overall postpartum DMI%BW and ECM and lesser EB from d 2 to 5 and from d 7 to 11 than cows that did not develop metritis. The main limitation in this study is that the time-order of disease relative to DMI%BW and ECM is inconsistent such that postpartum outcomes were measured before and after disease, which was diagnosed at variable intervals after calving. In summary, prepartum DMI%BW and EB were associated with and were predictors of metritis although the effect sizes were small for metritis, and calving disorders and metritis were associated with decreased DMI%BW and ECM postpartum.

Deciphering the rules of mRNA structure differentiation in Saccharomyces cerevisiae in vivo and in vitro with deep neural networks

The structure of mRNA in vivo is unwound to some extent in response to multiple factors involved in the translation process, resulting in significant differences from the structure of the same mRNA in vitro. In this study, we have proposed a novel application of deep neural networks, named DeepDRU, to predict the degree of mRNA structure unwinding in vivo by fitting five quantifiable features that may affect mRNA folding: ribosome density (RD), minimum folding free energy (MFE), GC content, translation initiation ribosome density (INI) and mRNA structure position (POS). mRNA structures with adjustment of the simulated structural features were designed and then fed into the trained DeepDRU model. We found unique effect regions of these five features on mRNA structure in vivo. Strikingly, INI is the most critical factor affecting the structure of mRNA in vivo, and structural sequence features, including MFE and GC content, have relatively smaller effects. DeepDRU provides a new paradigm for predicting the unwinding capability of mRNA structure in vivo. This improved knowledge about the mechanisms of factors influencing the structural capability of mRNA to unwind will facilitate the design and functional analysis of mRNA structure in vivo.

CellSim: a novel software to calculate cell similarity and identify their co-regulation networks

Background

Cell direct reprogramming technology has been rapidly developed with its low risk of tumor risk and avoidance of ethical issues caused by stem cells, but it is still limited to specific cell types. Direct reprogramming from an original cell to target cell type needs the cell similarity and cell specific regulatory network. The position and function of cells in vivo, can provide some hints about the cell similarity. However, it still needs further clarification based on molecular level studies.

Result

CellSim is therefore developed to offer a solution for cell similarity calculation and a tool of bioinformatics for researchers. CellSim is a novel tool for the similarity calculation of different cells based on cell ontology and molecular networks in over 2000 different human cell types and presents sharing regulation networks of part cells. CellSim can also calculate cell types by entering a list of genes, including more than 250 human normal tissue specific cell types and 130 cancer cell types. The results are shown in both tables and spider charts which can be preserved easily and freely.

Conclusion

CellSim aims to provide a computational strategy for cell similarity and the identification of distinct cell types. Stable CellSim releases (Windows, Linux, and Mac OS/X) are available at: www.cellsim.nwsuaflmz.com, and source code is available at: https://github.com/lileijie1992/CellSim/.

Evolutionary Analysis of the F-Box Gene Family in Saccharomycetaceae

F-box proteins are a core component of Skp1-Cul1-F-box (SCF) ubiquitin/ligase complexes and are involved in a lot of cellular processes in yeasts. However, the current knowledge of the molecular evolution of the F-box gene family in yeasts remains unclear. In this study, 136 F-box genes were identified in 10 yeast species of the Saccharomycetaceae. In addition to the F-box domain, the other six domains were identified in these F-box proteins. The evolutionary history of F-box gene numbers in 10 Saccharomycetaceae yeasts was reconstructed. Whole-genome duplication, interspersed repeats, and gene loss events were inferred. These events contributed to F-box gene number variation in the 10 yeast species. Eighty-seven and 33 positively selected sites were detected in program Selecton and Datamonkey web-server, respectively. Three of them were considered the significant positively selected sites, and 23 of them had changed radically in amino acid properties by using TreeSAAP. We investigated F-box gene number variation and underlying mechanisms, and selection patterns, all of which were beneficial to deeply understand genome evolution and figure out the function of the F-box proteins.

Effects of chronic dexamethasone exposure on bile acid metabolism and cecal epithelia function in goats

Bile acids (BAs) are synthesized in the liver via the oxidation of cholesterol and further metabolized by microbiota in the gut, where they simultaneously impact gut function. In the present study, 10 goats were randomly divided into 2 groups; 1 group was injected with dexamethasone (Dex; 0.2 mg/kg), and the other group was injected with saline as the control (Con) for 21 d. Expression levels of key genes and proteins in the liver and gut mucosa were analyzed and compared to investigate the impact of chronic stress on BA metabolism and related functions in ruminants. The results revealed that Dex decreased plasma total BAs (TBAs) concentration (P < 0.05) but increased TBA concentration in the cecal digesta (P < 0.05). Total cholesterol in the liver decreased moderately in response to Dex. The protein expression of cytochrome P450 family 7 subfamily A member 1 and cytochrome P450 family 27 subfamily A member 1, 2 enzymes that control BA synthesis in the liver, remained unchanged by Dex administration (P > 0.05). The expression of several genes in the cecal mucosa encoding epithelial tight junction proteins, including occludin (P < 0.05), tight junction protein 1 (P < 0.01), and claudin 1 (P < 0.05), increased significantly in response to Dex, and expression of defensin beta 1, which can strengthen the innate immune system, was also upregulated (P < 0.05). In addition, BAs increased the expression of the Solute Carrier family 9 member A 2 (P < 0.01) that encodes a sodium hydrogen exchanger. These results suggest that the Dex-induced disruption of BA homeostasis might be mediated through a liver-independent pathway in goats, and the Dex-induced accumulation of TBAs in the cecal digesta may improve volatile fatty acid transportation and mucosal defense.

Effect of varying prepartum dietary cation-anion difference and calcium concentration on postpartum mineral and metabolite status and milk production of multiparous cows

Eighty-two multiparous Holstein cows were enrolled 28 d before expected calving and assigned to 1 of 4 dietary treatments in a randomized block design experiment with a 2 × 2 factorial arrangement of treatments to determine the effect of feeding a neutral or acidogenic diet varying in Ca concentration on prepartum and postpartum intake, blood mineral and metabolite concentrations, and postpartum milk production. Prepartum diets were formulated to provide a dietary cation-anion difference (DCAD) of -21 (negative, NEG) or -2 (neutral, NEU) mEq/100 g of dry matter with either 1.3% or 1.8% Ca. After calving, cows remained on trial through 63 d in milk (DIM) and were fed a common lactation diet. Urine pH was lower for NEG compared with NEU and tended to be lower for 1.8% Ca compared with 1.3% Ca. Fractional excretion of Ca and Mg in urine was greater for NEG than for NEU. Prepartum plasma bicarbonate was lower and P was higher for NEG compared with NEU. Prepartum plasma P and blood urea nitrogen to creatinine ratio was higher for 1.3% compared with 1.8% Ca. Postpartum, concentrations of plasma total protein, albumin, blood urea nitrogen, Mg, and ionized Mg (iMg) were higher and Na was lower for NEU compared with NEG. An interaction of DCAD and Ca was observed for plasma creatinine, which was highest for cows fed NEU and 1.3% Ca compared with all other treatments. Interactions of DCAD and DIM were observed for plasma bicarbonate and iMg. Bicarbonate was higher at 3 DIM and lower at 14 DIM for NEU compared with NEG. Concentrations of iMg were higher at 1, 2, and 14 DIM for NEU compared with NEG. Interactions of Ca and DIM were observed for plasma Ca, Cl, and anion gap. Compared with cows fed 1.5% Ca, those fed 1.3% Ca had lower Ca and anion gap and higher Cl at 1 DIM and lower Cl and higher anion gap at 14 DIM. No differences were observed in body weight or body condition score due to DCAD or Ca. Prepartum dry matter intake (DMI) was lower for NEG compared with NEU and lower for 1.8% compared with 1.3% Ca. Postpartum DMI was not different among treatments. An interaction was observed for DCAD and DIM due to higher milk yield after 45 DIM for NEG compared with NEU. No differences were observed in milk component percentage or yield among treatments. There was an interaction of DIM and Ca for milk urea concentrations, which were higher at 5 wk and lower at 6 wk for 1.3% Ca compared with 1.8% Ca. These results suggest that feeding NEG prepartum alters plasma and urine mineral concentrations compared with feeding NEU and supports increased milk yield after 45 DIM. Feeding 1.8% Ca prepartum only improved plasma Ca at 1 DIM. Feeding either NEG or 1.8% Ca reduced DMI prepartum compared with NEU or 1.3% Ca.