Policy Disparities Between Singapore and Israel in Response to the First Omicron Wave.

Purpose: The purpose of this study is to evaluate public health measures during the first Omicron wave in Singapore and Israel to inform other countries confronted by COVID-19 outbreaks. Methods: A comparative analysis was conducted using epidemiological data from Singapore and Israel between November 25th, 2021 and May 2nd, 2022 and policy information to examine the effects of public health measures in the two countries during the COVID-19 pandemic. Results: Public health measures implemented by Singapore and Israel in response to the first Omicron wave were primarily intended to mitigate the effects of the COVID-19 pandemic. In Singapore, the pandemic led to more than 910,000 confirmed cases, a mortality rate of approximately 0.047%, a hospitalization rate of approximately 10.95%, and a severe illness rate of approximately 0.48%, without a second peak. In Israel, the pandemic not only resulted in over 2.74 million confirmed cases, a mortality rate of 0.095%, a hospitalization rate of about 7.39%, and a severe illness rate of approximately 2.30% but also returned after the significant relaxation of prevention regulations from March 1st, 2022. Conclusion: Early and strict border control measures and surveillance measures are more effective in preventing and controlling the rapid spread of new strains of COVID-19 in the early stage. Furthermore, to prevent and control this highly infectious disease, COVID-19 vaccinations and booster shots must be promoted as soon as possible, medical service capacity must be enhanced, the hierarchical medical system must be improved, and non-pharmacological interventions must be implemented.

Genome re-sequencing reveals the evolutionary history of peach fruit edibility.

Peach (Prunus persica) is an economically important fruit crop and a well-characterized model for studying Prunus species. Here we explore the evolutionary history of peach using a large-scale SNP data set generated from 58 high-coverage genomes of cultivated peach and closely related relatives, including 44 newly re-sequenced accessions and 14 accessions from a previous study. Our analyses suggest that peach originated about 2.47 Mya in southwest China in glacial refugia generated by the uplift of the Tibetan plateau. Our exploration of genomic selection signatures and demographic history supports the hypothesis that frugivore-mediated selection occurred several million years before the eventual human-mediated domestication of peach. We also identify a large set of SNPs and/or CNVs, and candidate genes associated with fruit texture, taste, size, and skin color, with implications for genomic-selection breeding in peach. Collectively, this study provides valuable information for understanding the evolution and domestication of perennial fruit tree crops.

Influence of pCP1NetB ancillary genes on the virulence of Clostridium perfringens poultry necrotic enteritis strain CP1.

BACKGROUND: Necrotic enteritis (NE) is an economically important disease of poultry caused by certain Clostridium perfringens type A strains. The NetB toxin plays a critical role in the pathogenesis of NE. We previously demonstrated that netB is located within a 42 kb plasmid-encoded pathogenicity locus (NELoc-1), which also encodes 36 additional genes. Although NetB clearly plays a role in pathogenesis, the involvement of the other NELoc-1 genes has not yet been established. The current study was to provide experimental evidence to confirm the involvement of these genes in NE pathogenesis. RESULTS: The present study has characterized a virulent C. perfringens strain (CP1) that has spontaneously lost the NELoc-1-encoding plasmid, pCP1netB. When assessed for cytotoxicity on Leghorn Male Hepatoma (LMH) cells, the culture supernatant of the pCP1netB-deficient CP1 variant (CP1ΔpCP1netB) demonstrated significantly reduced cytotoxicity compared to the wild-type. In addition, CP1ΔpCP1netB was unable to cause intestinal lesions in chickens in a NE disease model. When netB alone was introduced into CP1ΔpCP1netB, in vitro cytotoxicity was restored to the wild-type level; however, it did not completely restore virulence when used to challenge broiler chickens [mean lesion score of 0.71 compared to 3.23 in the wild type control group (n = 14)]. CONCLUSIONS: The results of this study suggest that other genes present in NELoc-1, in addition to netB, are required for full virulence in the chicken challenge model.

[Identification of soft rot pathogens on Chinese cabbage [Brassica campestris L. ssp. chinensis (L.) Makino var. communis Tsen et Lee] in Beijing].

OBJECTIVE: This study aimed to identify soft rot pathogens of Chinese cabbage [Brassica campestris L. ssp. chinensis (L.) Makino var. communis Tsen et Lee] in Beijing. METHODS: The 40 strains isolated from Tongzhou and Daxing districts in Beijing were characterized by morphological, biological, biochemical and physiological methods, 16S rRNA sequence as well as 16S-23S rRNA intergenic spacer (IGS) region analysis. RESULTS: The strains belonged to two different Pectobacterium carotovorum subspecies: 13 strains of them belonged to Pectobacterium carotovorum subsp. carotovorum (Pcc) and the other 27 strains belonged to Pectobacterium carotovorum subsp. brasiliensis (Pcb). The results of Chinese cabbage (Brassica campestris L. ssp. pekinensis) pathogenicity test showed that the strains in the same subspecies, origins and 16S rRNA gene sequences had significant differences in pathogenicity. CONCLUSION: Pectobacterium carotovorum subsp. carotovorum and Pectobacterium carotovorum subsp. brasiliensis were the soft rot pathogens on Chinese cabbage [ Brassica campestris L. ssp. chinensis(L.) Makino var. communis Tsen et Lee] in Beijing. It was the first report that Pectobacterium carotovorum subsp. brasiliensis (Pcb) caused soft rot disease on cabbage in China.

Ax21-triggered immunity plays a significant role in rice defense against Xanthomonas oryzae pv. oryzicola.

XA21, as a pattern recognition receptor in rice, senses the quorum-sensing (QS) signal molecule Ax21 secreted by Xanthomonas oryzae pv. oryzae (Xoo) and mediates hypersensitive response-like immunity against the pathogen. However, for the infection of another pathovar, X. o. pv. oryzicola (Xoc), relatively weak defense responses are observed in XA21-containing rice cultivars. In the present study, we demonstrated that the Xoc Δax21 mutant caused more severe disease symptoms than the wild type in XA21 rice cv. IRBB21, but not in non-Xa21 rice cv. Taipei 309. The substance(s) secreted by the wild-type Xoc strain, but not those by the ax21 mutant triggered host immunity against Xoo PXO99 Δax21 in Xa21 rice. Immunoblot analysis corroborated that Xoc, like Xoo, synthesizes and secretes Ax21. Furthermore, the membrane fusion protein RaxA was demonstrated to be required, but the ATP-binding cassette transporter RaxB was dispensable for Ax21 secretion in Xoc. In addition, we demonstrated that Ax21 functions as a QS signal molecule that regulates biofilm formation in Xoc. However, Ax21 signaling is dispensable for bacterial motility, the production of extracellular polysaccharide and protease secretion in Xoc. Interestingly, the two-component system RaxR/H was involved in the regulation of bacterial motility and the regulation was likely independent on Ax21 signaling in Xoc. Taken together, the results indicated that Ax21 secreted by Xoc might induce plant immunity that plays a significant role in rice defense against the pathogen infection.

Identification of putative virulence-associated genes of Haemophilus parasuis through suppression subtractive hybridization.

Haemophilus parasuis is the causative agent of Glässer's disease. Up to now 15 serovars of H. parasuis have been identified, with significant differences existing in virulence between serovars. In this study, suppression subtractive hybridization (SSH) was used to identify the genetic difference between Nagasaki (H. parasuis serovar 5 reference strain, highly virulent) and SW114 (H. parasuis serovar 3 reference strain, non-virulent). A total of 191 clones were obtained from the SSH library. Using dot hybridization and PCR, 15 clones were identified containing fragments that were present in the Nagasaki genome while absent in the SW114 genome. Among these 15 fragments, three fragments (ssh1, ssh13, ssh15) encode cell surface-associated components; three fragments (ssh2, ssh5, ssh9) are associated with metabolism and stress response; one fragment (ssh8) is involved in assembly of fimbria and one fragment (ssh6) is a phage phi-105 ORF25-like protein. The remaining seven fragments are hypothetical proteins or unknown. Based on PCR analysis of the 15 serovar reference strains, eight fragments (ssh1, ssh2, ssh3, ssh6, ssh8, ssh10, ssh11 and ssh12) were found in three to five of most virulent serovars (1, 5, 10, 12, 13 and 14), zero to two in three moderately virulent serovars (2, 4 and 15), but absent in the low virulent serovar (8) and non-virulent serovars (3, 6, 7, 9 and 11). In vivo transcription fragments ssh1, ssh2, ssh8 and ssh12 were identified in total RNA samples extracted from experimental infected pig lung by RT-PCR. This study has provided some evidence of genetic differences between H. parasuis strains of different virulence.

[Regulation pattern of the FRUITFULL (FUL) gene of Arabidopsis thaliana].

FRUITFULL (FUL) is an MADS box gene that functions early in controlling flowering time, meristem identity and cauline leaf morphology and later in carpel and fruit development in Arabidopsis thaliana. In order to clarify the regulation of FUL expression the upstream regulatory region, -2148 bp - +96 bp and the first intron of the FUL gene were cloned, and vectors with a series of deletion of FUL promoter, and the ones fused with the first intron were constructed. Vectors harboring the fusion of cis-acting elements with the constitutive promoters of TUBULIN and ACTIN were also constructed. Beta-Glucuronidase activity assays of the transgenic Arabidopsis plants showed that two cis-elements were involved in the repression of FUL expression, with one of the two being probably the binding site of the transcriptional factor AP1. And the two CArG boxes played a important role in FUL initiation particularly. Furthermore, the first intron of FUL was shown to participate in the development of carpel and stamen as an enhancer.

Molecular cloning, identification, and chromosomal localization of two MADS box genes in peach (Prunus persica).

MADS box proteins play an important role in floral development. To find genes involved in the floral transition of Prunus species, cDNAs for two MADS box genes, PpMADS1 and PpMADS10, were cloned using degenerate primers and 5'- and 3'-RACE based on the sequence database of P. persica and P. dulcis. The full length of PpMADS1 cDNA is 1,071 bp containing an open reading frame (ORF) of 717 bp and coding for a polypeptide of 238 amino acid residues. The full length of PpMADS10 cDNA is 937 bp containing an ORF of 633 bp and coding for a polypeptide of 210 amino acid residues. Sequence comparison revealed that PpMADS1 and PpMADS10 were highly homologous to genes AP1 and PI in Arabidopsis, respectively. Phylogenetic analysis indicated that PpMADS1 belongs to the euAP1 clade of class A, and PpMADS10 is a member of GLO/PI clade of class B. RT-PCR analysis showed that PpMADS1 was expressed in sepal, petal, carpel, and fruit, which was slightly different from the expression pattern of AP1; PpMADS10 was expressed in petal and stamen, which shared the same expression pattern as PI. Using selective mapping strategy, PpMADS1 was assigned onto the Bin1:50 on the G1 linkage group between the markers MCO44 and TSA2, and PpMADS10 onto the Bin1:73 on the same linkage group between the markers Lap-1 and FGA8. Our results provided the basis for further dissection of the two MADS box gene function.

[Isolation and identification of a Pp-LIM only A gene expressed during cold acclimation in Physcomitrella patens].

Cold acclimation can improve freezing tolerance. Here cDNA amplified fragment length polymorphism (cDNA-AFLP) was used to isolate differentially expressed cDNAs and a Pp-LIM only A cDNA was isolated and identified in the cold acclimation of Physcomitrella patens. Real-time RT-PCR indicated it is obviously up-regulated at 6 h, 12 h, 24 h, 48 h and 72 h after cold acclimation. After comparing the cDNA with the gene sequence, seven introns and eight exons were identified in the cDNA. The cDNA putatively encodes a protein of 345 amino acid residues and only contains one LIM domain which has highly similarity with the PDZ/LIM domains of the protein family in animals. We proposed that Pp-LIM only A be a new gene coding for the LIM-domain containing protein and enhance stability of cell membrane via their effects on cytoskeleton during cold acclimation in P. patens.

Differentially expressed genes under cold acclimation in Physcomitrella patens.

Cold acclimation improves freezing tolerance in plants. In higher plants, many advances have been made toward identifying the signaling and regulatory pathways that direct the low-temperature stress response; however, similar insights have not yet been gained for simple nonvascular plants, such as bryophytes. To elucidate the pathways that regulate cold acclimation in bryophytes, we used two PCR-based differential screening techniques, cDNA amplified fragment length polymorphism (cDNA-AFLP) and suppression subtractive hybridization (SSH), to isolate 510 ESTs that are differentially expressed during cold acclimation in Physcomitrella patens. We used realtime RT-PCR to further analyze expression of 29 of these transcripts during cold acclimation. Our results show that cold acclimation in the bryophyte Physcomitrella patens is not only largely similar to higher plants but also displays distinct differences, suggests significant alteration during the evolution of land plants.

SSR allelic variation in almond (Prunus dulcis Mill.).

Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

[Cloning and characterization of two MADS box genes from peach (Prunus persica)].

With the aim of finding genes involved in the floral transition of Prunus species (Prunus sp.), the EST (expressed sequence tags) sequences were extracted from the public databases. Eight MADS box genes' cDNAs were obtained. Two of them, PpMADS4 and PpMADS6 (The accession numbers in GenBank are AY705972 and AY705973), were cloned from peach (Prunus persica). The full length cDNA of PpMADS4 is 850 bp long. It contains an open reading frame of 732 bp, coding for a polypeptide of 243 amino acids. The full length cDNA of PpMADS6 is 1,190 bp long. It contains an open reading frame of 768 bp coding for a polypeptide of 256 amino acids. PpMADS4 closely resembles the Arabidopsis AGAMOUS gene. It is an AGAMOUS-like C class MADS box gene, and it expresses in petal, carpel, fruit and nutlet as demonstrated by RT-PCR analysis. PpMADS6 is likely to be the peach orthologue of the Petunia PFG genes and it is an A class MADS box gene. It has been shown with RT-PCR that it expresses in leaf, sepal, petal, carpel and fruit. It may be involved in the transition from the juvenile to the adult stage.

Development of SSR markers for the phylogenetic analysis of almond trees from China and the Mediterranean region.

Expressed sequence tag (EST) derived simple sequence repeats (SSRs, microsatellites) were screened and identified from 3863 almond and 10 185 peach EST sequences, and the spectra of SSRs in the non-redundant EST sequences were investigated after sequence assembly. One hundred seventy-eight (12.07%) almond SSRs and 497 (9.97%) peach SSRs were detected. The EST-SSR occurs every 4.97 kb in almond ESTs and 6.57 kb in peach, and SSRs with di- and trinucleotide repeat motifs are the most abundant in both almond and peach ESTs. Twenty one EST-SSRs were thereafter, developed and used together with 7 genomic SSRs, to study the genetic relationship among 36 almond (P. communis Fritsch.) cultivars from China and the Mediterranean area, as well as 8 accessions of other related species from the genus Prunus. Both EST-derived and genomic SSR markers showed high cross-species transferability in the genus. Out of the 112 polymorphic alleles detected in the 36 cultivated almonds, 28 are specific to Chinese cultivars and 25 to the others. The 44 accessions were clustered into 4 groups in the phylogenetic tree and the 36 almond cultivars formed two distinct subgroups, one containing only Chinese cultivars and one of unknown origin and the other only those originating from the Mediterranean area, indicating that Chinese almond cultivars have a distinct evolutionary history from the Mediterranean almond. Our preliminary results indicated that common almond was more closely related to peach (P. persica (L.) Batsch.) than to the four wild species of almond, (P. mongolica Maxim., P. ledebouriana Schleche, P. tangutica Batal., and P. triloba Lindl.). The implications of these SSR markers for evolutionary analysis and molecular mapping of Prunus species are discussed.

Analysis of genetic variation in Ganoderma lucidum after space flight.

A modified CTAB method was used in the extraction of total cellular DNA of Ganoderma lucidum. Four strains Cx, Ch, C3 and C4, and their counterparts, four space flown strains Sx, Xh, S3 and S4, were analysed by amplified fragment length polymorphism (AFLP) with several primer combinations. Polymorphic bands were detected between Sx and Cx, S3 and C3, respectively. Somatic incompatibility tests further confirmed their heterogeneity. However, no disparity between Sh and Ch, S4 and C4 was detectable. The results suggest that spaceflight may be used to accelerate breeding of Ganoderma lucidum strains for commercial cultivation.