Serum Biochemical Reference Values for Adult and Non-adult Chinese Alligators during the Deep and Late Hibernation Periods

Background: The Chinese alligator (Alligator sinensis) is a critically endangered species. Due to the rapid growth of the captive population, the susceptibility to disease during the recovery period after winter hibernation, especially in young alligators, have detrimentally affected Chinese alligator populations. Serum biochemistry, which relates to metabolism, nutritional status and disease, is enormously helpful in evaluating physical conditions in reptile. Many studies have reported the serum biochemical reference values of various reptilian species, including several crocodilians. However, reference values for Chinese alligators have not yet been reported. For captive Chinese alligators, hibernation is a crucial period because winter management has a direct influence on the survival rate of juveniles and the reproduction rate of adults. The main object of the present study refore was to measure the serum biochemical values of captive Chinese alligators during hibernation.Materials, Methods & Results: As such, this study investigates the serum biochemistry as a factor of age and hibernation stage. During the deep and late hibernation periods blood samples were drawn from 30 healthy captive Chinese alligators (adults, sub-adults, and juveniles) at the Anhui Research Center of Chinese Alligator Reproduction (ARCCAR). Serum biochemical measurements were performed using an automated biochemical analyzer and compared based on the age group and hibernation stage via two-way ANOVA. During late hibernation, serum lactate dehydrogenase, alkaline phosphatase, and aspartate aminotransferase activity increased in all age groups in comparison to that in deep hibernation, while the concentration of calcium decreased. Meanwhile, the concentration of serum phosphorus, uric acid, total protein, and globulin in sub-adults and juveniles considerably increased in comparison to that in deep hibernation, while cholesterol and albumin declined. However, in adults only slight changes were noted. Based on comprehensive statistical analysis, our results indicate that sub-adults and juveniles are at risk of developing renal disease during artificial hibernation.Discussion: Chinese alligators, especially sub-adults and juveniles, are particularly vulnerable to disease when they wake from hibernation. They often display symptoms such as depression, anorexia, lethargy, sluggish movement, slow, incremental weight gain, progressive muscle wasting, and even death. The high rate of morbidity in non-adult Chinese alligators may be associated with the high density of UA and other changes in multiple biochemical markers that occur during late hibernation. These altered serum biochemical profiles may indicate kidney damage. One of the most common diseases among reptiles is nephropathy, the symptoms of which are non-specific and tend to agree with those observed post-hibernation. In summary, this study has reported the serum biochemical values of Chinese alligators of varying ages in the deep and late hibernation phases. Based on statistical analyses, interesting differences between the serum biochemical values of adults and non-adults during the deep and late hibernation have been found. The observed changes suggest that, under an artificial hibernation environment, the kidneys of sub-adults and juveniles may become impaired. We believe that the data reported in this study will provide clinical guidance to facilitate more appropriate artificial wintering conditions for Chinese alligators, and assist the breeding and management of these reptiles, as well as disease prevention, during hibernation and recovery

A unified fused Lasso approach for sparse and blocky feature selection in regression and classification

In many applications, sparse and blocky coefficients often occur in regression and classification problems. The fused Lasso was designed to recover these sparse structured features especially when the design matrix encounters the situation of ultrahigh dimension. Quantile loss is well known as a robust loss function in regression and classification. In this paper, we combine quantile loss and fused Lasso penalty together to produce quantile fused Lasso which can achieve sparse and blocky feature selection in both regression and classification. Interestingly, our proposed model has the unified optimization formula for regression and classification. For ultrahigh dimensional collected data, we derive multi-block linearized alternating direction method of multipliers (LADMM) to deal with it. Moreover, we prove convergence and derive convergence rates of the proposed LADMM algorithm through an elegant method. Note that the algorithm can be easily extended to solve many existing fused Lasso models. Finally, we present some numerical results for several synthetic and real world examples, which illustrate the robustness, scalability, and accuracy of the proposed method

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

Most published genome sequences are drafts, and most are dominated by computational gene prediction. Draft genomes typically incorporate considerable sequence data that are not assigned to chromosomes, and predicted genes without quality confidence measures. The current Actinidia chinensis (kiwifruit) 'Hongyang' draft genome has 164\ua0Mb of sequences unassigned to pseudo-chromosomes, and omissions have been identified in the gene models

The role of the SVP gene family in controlling bud dormancy

SHORT VEGETATIVE PHASE (SVP)-like genes in the StMADS11 gene family have roles in the regulation of flowering time in annual plants and there is evidence that they also function in the regulation of dormancy in perennials. Expression patterns of SVP-like DORMANCY-ASSOCIATED MADS-BOX (DAM) genes in some Prunus species indicate their role in dormancy and their deletion is likely responsible for the non-dormant, evergrowing peach phenotype. As these Prunus species are recalcitrant to transformation, the hypothesis that SVP genes regulate dormancy could not be tested by transgenic overexpression. Kiwifruit (Actinidia spp.) SVP-like genes are predominantly expressed in axillary buds at the dormant stage and have been described as potential homologs of DAM genes, indicating they might be involved in controlling dormancy in kiwifruit. This study examined the function of the kiwifruit AcSVP2 gene by overexpressing it in two kiwifruit species with different chilling requirements for spring budbreak and in annual tobacco. The results suggest that in the high-chill kiwifruit A. chinensis var. deliciosa AcSVP2 has no significant effect on establishing dormancy, but delays budbreak. This delay in budbreak can be overcome by sufficient chilling. Overexpression of AcSVP2 in the low-chill kiwifruit species A. eriantha, had minimal effect and in transgenic tobacco it reduced plant height, delayed root growth and seed germination, but did not affect flowering time. Transcriptomic analyses (RNA-seq) of AcSVP2 transgenic lines during dormancy revealed that many of AcSVP2 regulated genes are involved in stress responses, mostly osmotic and cold response genes, with a subset also identified as ABA-responsive genes. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) of AcSVP2 transgenic lines showed that AcSVP2 directly binds to many target genes that function in a range of biological processes, especially those involved in repressing meristem activity and ABA-mediated dehydration pathways. AcSVP2 targeted genes also largely overlap with Arabidopsis SVP targeted genes expressed during vegetative growth and flower development. This suggests a conserved mechanism of action exists between SVP genes of taxonomically distant plants. Two regulatory systems associated with the control of AcSVP2 expression were studied: epigenetic regulation by histone modification was examined using chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) and regulation mediated by transcription factors (TFs) was investigated using in vivo Nicotiana benthamiana transient assays. Results from the ChIP-qPCR experiments showed that accumulation and reduction of trimethylated H3K4 (H3K4me3) and acetylated H3 (H3ac) correlated with the expression of AcSVP2 during dormancy in kiwifruit (A. chinensis). A 2.3kb AcSVP2 promoter region was used to screen 101 kiwifruit transcription factors and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1)-like genes, and potential candidate genes of bZIP, NAC, and MYB in the osmotic and abscisic acid signalling pathway were identified as possible regulators of AcSVP2 expression. Cis-regulatory elements (CREs) were identified in a 2.3kb AcSVP2 promoter region, including MADS-box protein binding elements, CArG-boxes, ABA response elements (ABRE), and drought response TFs binding motifs (MYCATERD1), and are likely to represent the binding sites of the TFs investigated. Kiwifruit AcSVP family genes, AcSVP1 and AcSVP4, showed elevated expression over the period of winter dormancy. Similar to AcSVP2, overexpression of AcSVP1 and AcSVP4 in the high-chill kiwifruit A. chinensis var. deliciosa, also delayed budbreak in spring, but had no effect on budbreak and flowering in the low-chill A. eriantha. Overexpression of AcSVP1 in tobacco ‘Maryland Mammoth’ significantly delayed flowering and seed germination, while AcSVP4 only had a minor effect on flowering and seed germination. Analysis of cis-regulatory motifs in the promoter regions of AcSVP1 and AcSVP4 and promoter transactivation assay revealed that expression of AcSVP1 and AcSVP4 may be controlled by transcription factors, similar to those identified as possible regulators of AcSVP2. These results suggests a conserved regulatory mechanism and a synergistic role for kiwifruit AcSVP1, AcSVP2 and AcSVP4 in preventing premature kiwifruit budbreak during winter. Interrogation of SVP-like genes in apple (Malus × domestica ‘Royal Gala’) genome confirmed that there are three DAM-like and two SVP-like genes. Expression analysis in apical buds of ‘Sciros’ apple trees over the seasons revealed that transcripts of MdDAMa and MdDAMc were elevated in the early autumn, and mostly absent over the winter and spring months. MdDAMb, MdSVPa and MdSVPb were expressed in the winter. Ectopic expression of MdDAMb and MdSVPa in ‘Royal Gala’ apple plants resulted in delayed budbreak in spring. Overall, the findings of this study have advanced our understanding of the roles the SVP/DAM-like genes play in the dormancy process of woody perennials

Multiresidue Pesticide Analysis in Tea Using GC–MS/MS to Determine 12 Pesticide Residues (GB 2763-2021)

Pesticides are widely used on tea plants, and pesticide residues are of significant concern to consumers. The National Food Safety Standard Maximum Residue Limits for Pesticides in Food (GB 2763-2021) was recently amended. However, detection methods for pesticides newly added to the list of residues in beverages have not yet been established. For that reason, this study developed a solid-phase extraction (SPE) and gas chromatography–tandem mass spectrometry (GC–MS/MS) method for determining the residues of 12 pesticides, including four newly added, in black and green tea. Sample preparation processes (sample extraction, SPE clean-up, elution solvent, and elution volume) were optimized to monitor these residues reliably. Multiple reaction monitoring (MRM) was used for GC–MS/MS electron impact (EI) mode determination. Finally, satisfactory recoveries (70.7–113.0% for green tea and 72.0–99.1% for black tea) were achieved at three concentrations (10 μg/kg, 20 μg/kg, and 100 μg/kg). The LOQs were 0.04–8.69 μg/kg, and the LODs were 0.01–3.14 μg/kg. This study provides a reliable and sensitive workflow for determining 12 pesticide residues in tea, filling a gap in the newly revised National Standards

Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs-2

<p><b>Copyright information:</b></p><p>Taken from "Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs"</p><p>http://www.plantmethods.com/content/3/1/12</p><p>Plant Methods 2007;3():12-12.</p><p>Published online 12 Oct 2007</p><p>PMCID:PMC2225395.</p><p></p>). An ethidium bromide-stained prominent band of tRNA was used as the loading control (LC). B. Stem-loop end-point RT-PCR analyses of miRNA expression. miRNAs were amplified using 28 cycles of PCR. Pumpkin () mRNA was amplified using 30 cycles of standard PCR. C. Stem-loop end-point RT-PCR analyses of miRNA expression in pumpkin phloem sap. The number of PCR cycles is indicated on the top. miR156, miR159 and miR167, but not miR171 were detected

Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs-4

<p><b>Copyright information:</b></p><p>Taken from "Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs"</p><p>http://www.plantmethods.com/content/3/1/12</p><p>Plant Methods 2007;3():12-12.</p><p>Published online 12 Oct 2007</p><p>PMCID:PMC2225395.</p><p></p>d detectable amplicons after 40 PCR cycles. B. UPL probe assay for miR166. No fluorescence was detected in the negative control reactions after 45 cycles of PCR. C. UPL probe assay amplification products for miR166 separated by gel electrophoresis on 4% agarose showing specific and non-specific amplification bands obtained after 45 cycles of PCR. Arrowhead indicates the expected size of amplicons. 1, 20 ng RNA; 2, 2 ng RNA; 3, 200 pg RNA; 4, 20 pg RNA; 5, 20 ng RNA minus-RT control; 6, water control

Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs-1

<p><b>Copyright information:</b></p><p>Taken from "Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs"</p><p>http://www.plantmethods.com/content/3/1/12</p><p>Plant Methods 2007;3():12-12.</p><p>Published online 12 Oct 2007</p><p>PMCID:PMC2225395.</p><p></p>low molecular weight (L) RNA were purified from 20 μg of total RNA, separated by electrophoresis, transferred and hybridised with miR156 antisense probe. B. Stem-loop RT-PCR analyses of miR156 expression. 200 ng total RNA (T), high molecular weight RNA purified from 200 ng total RNA (H) and low molecular weight RNA purified from 200 ng total RNA (L) were subjected to stem-loop RT PCR. The amount of input RNA as measured by NanoDrop is indicated below. PCR cycle numbers are indicated to the left. SA, shoot apex; S, stem: L, leaf

Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs-0

<p><b>Copyright information:</b></p><p>Taken from "Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs"</p><p>http://www.plantmethods.com/content/3/1/12</p><p>Plant Methods 2007;3():12-12.</p><p>Published online 12 Oct 2007</p><p>PMCID:PMC2225395.</p><p></p>se probe. B. Stem-loop RT-PCR analyses of miR156, miR159 and miR167 expression. The amounts of RNA used for reverse transcription reactions are indicated on the top. PCR cycle numbers are indicated on the left