Monthly Archives: November 2023

Identification of variants and haplotypes of the Rf4 locus in rice cultivars

Our and others previous studies identified five variants at the Rf4 locus, namely, Rf4M and Rf4I (in indica fertile restorer lines), rf4aus (in circum-aus rice, see below), rf4i (in indica CMS-WA/maintainer lines), and rf4j (in japonica rice)15,17,18. To further reveal the origin and evolution of the Rf4 locus, we re-analyzed the genome sequences of the Rf4 locus using publicly available rice genome information for ZS97B (Zhenshan97B, a maintainer line with rf4i) (http://rice.hzau.edu.cn/rice_rs3/)23, Nip (Nipponbare, a japonica line with rf4j) (https://rapdb.dna.affrc.go.jp/)38,39, and MH6323 and SH498 (https://www.mbkbase.org/rice)40 (Shuhui498, fertility restorer line carrying functional Rf4). We focused on part of a PPR cluster that includes the Rf4 locus based on the reference genome of the restorer line MH63 (Fig.1a).

a Homologous gene relationship (microsynteny block) at the Rf4 locus in O. sativa ssp. indica and O. sativa ssp. japonica. b Different haplotypes of the Rf4 complex locus region involving in the Rf4a-copy (Copy-a) and Rf4b-copy (Copy-b) identified in Asian cultivated rice. Gray background shows other PPR genes, white background shows non-functional rf4 variants, black background shows functional Rf4 variants. j: japonica, aus:circum- aus, i: indica, I: IR24, M: MH63, Nip: Nipponbare (a japonica variety). IR24 and MH63 are indica restorer lines.

At the Rf4 locus region, we first examined two lines that lack the ability to restore fertility and identified three PPR genes (PPR7 [Os10g0495400], rf4j [Os10g0495200], and PPR10 [Os10g0495100]) in Nip (Fig.1a) and three PPR genes (PPR7, rf4i, PPR10) in ZS97B (Fig.1a). The rf4i variant was pseudogenized and non-functional due to the presence of a premature termination codon (Fig.1a).

We next examined two lines that have the ability to restore fertility. The Rf4 locus regions of MH63 and SH498 possess seven PPR genes, in addition to previously known functional Rf4 variant (here defined as Rf4a, of functional Rf4 in Copy-a site of Rf4 locus), PPR7, PPR8, and three copies of PPR10 genes, which included another functional Rf4 variant Rf4b identified in the Copy-b site of Rf4 locus (Fig.1a). The interval between Rf4a and Rf4b is 74.8kb, and the Rf4a and Rf4b coding sequences show 100% amino acid identity. The regions 7.5kb upstream of the start codon and 1.5kb downstream of the stop codon of Rf4a and Rf4b showed 98.4% and 99.7% similarity, respectively (Supplementary Data1). These findings reveal that different rice varieties show SV and CNV at the Rf4 locus.

Then, we further investigated SV and CNV at the Rf4 locus region in 311 rice cultivars by PCR amplification and sequencing. To this end, we designed site-specific PCR primers based on single-nucleotide polymorphisms (SNPs, Supplementary Table1). The Rf4a and Rf4b genes were amplified using a common primer F1 combined with the site-specific reverse primers a-R and b-R, respectively; the rf4i fragment was amplified using a primer pair F2 and i-R (Fig.1a). In total, there were seven variants and eight haplotypes (H1H8) based on the combination of the Copy-a and Copy-b variants at the Rf4 locus in the modern rice cultivars (Fig.1b and Supplementary Data2). Sequence analyses demonstrated that the restorer lines contain five haplotypes with one- or two-copy Rf4 variants, including Rf4aI (H2), Rf4bM (H6), Rf4aM-Rf4bM (H1), Rf4aI-rf4b (H7), and rf4a-Rf4bM (H8), while all current CMS-WA lines (and their maintainer lines) carry the rf4i (H4) variant; the rf4j (H5) variant is present mainly in japonica cultivars. Among these variants, rf4aus was previously named as H318 (Fig.1b).

To trace the evolutionary history of Rf4 in the Oryza genus, we further investigated the CNV and sequence polymorphisms of Rf4 and rf4 variants among wild rice and landrace rice accessions. In addition to the seven Rf4 and rf4 variants identified in the cultivars, 61 variants were identified in the Copy-a and/or Copy-b sites of the Rf4 locus (from GG to AA-genome species) (Supplementary Data25), pointing to the prevalence of SV and CNV in the Rf4 locus.

We then performed a BLAST search for putative orthologs and homologs of Rf4 and rf4 in Poaceae genomes in the GenBank database (https://www.ncbi.nlm.nih.gov/). The putative homologs in Aegilops tauschii, Setaria italica, Setaria viridis, Sorghum bicolor, Triticum aestivum, Triticum dicoccoides, and Zea mays were similar to the rice Rf4 and rf4 variants (Supplementary Fig.1). The homologous gene LOC117839145 of S. viridis shared the highest nucleotide sequence similarity of 72.2% with the Rf4M variants in the rice cultivars (Supplementary Data6).

We next used the nucleotide sequences to construct a phylogenetic tree of Rf4 and rf4 in the Oryza genus using LOC117839145 (S. viridis) as the outgroup. The variants of different species were divided into six homologous lineages (Supplementary Fig.2). Among these, the rf4i, rf4a, and rf4b clades were closely related to each other, and Rf4M and Rf4I were in the same clade, whereas the lineages containing rf4aus and rf4j were closely related (Supplementary Fig.2). During the evolution of wild rice, a considerable number of rf4a, rf4b, and Rf4 variants were developed, but only two variants each of rf4j and rf4i were generated (Supplementary Fig.2). Among Rf4 variants in the different rice cultivars, rf4a, rf4b, rf4aus, rf4i, and Rf4 mainly occur in the indica group, rf4j mainly occurs in the japonica group, and rf4i was only found in bred maintainer lines and CMS-WA lines (Supplementary Data2).

In the wild rice O. meyeriana (GG-genome), only a putative one-copy Rf4 variant appeared at the Copy-a site, but not the Copy-b site, thus, this Copy-a variant sequence likely represents the primitive sequence of ancestral Rf4, which we named Anc-Rf4 (Fig.2 and Supplementary Data3). Along with sequence variation and genetic recombination, various haplotypes (H13-H68) consisting of Rf4-like and/or rf4-like variants were generated in the genomes of EE (O. australiensis), CCDD (O. alta, O. grandiglumis, and O. latifolia), CC (O. eichingeri, O. officinalis, and O. rhizomatis), BBCC (O. minuta), BB (O. punctata), and AA genomes (O. meridionalis, O. glumaepatula, O. rufipogon, and O. nivara) of these wild species (Fig.2 and Supplementary Data3); including one-copy haplotypes Rf4a/rf4a-likes (a group of Rf4a-like or rf4a-like variants with SNPs) at the Copy-a site, and Rf4b/rf4b-likes (a group of Rf4b-like or rf4b-like variants with SNPs) at the Copy-b site (H13-H27) (Fig.2 and Supplementary Data3). Further, various two-copy haplotypes containing Rf4-like and/or rf4-like variants were formed, including Rf4aM-rf4b-likes, rf4a-likes-Rf4bM, rf4a-likes-Rf4b-likes, Rf4a-likes-Rf4b-likes, and rf4a-likes-rf4b-likes (H28-H68) (Fig.2 and Supplementary Data3). However, no Rf4 and rf4 variants were detected in the tested O. longistaminata, O. barthii, and O. glaberrima accessions at the Copy-a or Copy-b sites (Fig.2 and Supplementary Data2 and 3). The variants such as rf4i, Rf4aI, and rf4b were first identified in O. australiensis (EE-genome), while Rf4M and rf4j were first identified in O. officinalis (CC-genome), and rf4aus and rf4a appeared only in indica in O. sativa (Fig.2 and Supplementary Data24).

Current Rf4 haplotypes may have originated from an ancestral type of Rf4 (Anc-Rf4, H69), which first emerged at Copy-a in the oldest wild rice O. meyeriana (GG-genome). Sequence variation, gene duplication, and recombination events resulted in new one-copy (H12-H27) or two-copy (H28-H68) haplotypes of R/rf4a-likes (a group of Rf4a-like or rf4a-like variants with SNPs) and/or R/rf4b-likes (a group of Rf4b-like or rf4b-like variants with SNPs) in wild rice. During evolution, along with natural and human selections, the nascent one-copy and two-copy Rf4 and/or rf4 haplotypes gradually migrated into the lineages of O. rufipogon, O. nivara, and O. sativa. Rf4 haplotypes were not detected in tested accessions of O. longistaminata, O. barthii, and O. glaberrima. Among the eight Rf4 haplotypes (H1H8) in modern cultivars, three two-copy haplotypes (indicated by asterisks *, the percentages on the left showed frequency of specific haplotype in the tested accessions) are predominant in restorer lines. H1 (Rf4aM-Rf4bM) and H7 (Rf4aI-rf4b) haplotypes first appeared in O. nivara and O. australiensis (EE-genome), respectively, while H8 (rf4a-Rf4bM) is present only in landraces and modern cultivars of O. sativa. The one-copy variant Rf4aI in H2 of modern cultivars was only found in H7, suggesting that H2 may be derived from loss of rf4b in H7 from O. rufipogon. Other one-copy haplotypes such as H3 (rf4aus), H4 (rf4i), H5 (rf4j) and H6 (Rf4bM) first emerged in O. sativa, O. australiensis, O. officinalis (CC-genome), and O. glumaepatula (AA-genome), respectively. The number in the brackets next to each species represents frequency of the haplotypes detected in the species. MYA: million years ago (divergence time).

To confirm the biological functions of the rf4 haplotypes in the rice cultivars, we analyzed amino acid sequence variation among six proteins: rf4a, rf4b, rf4j, rf4aus, Rf4M, and rf4i. Whereas rf4i is a truncated product containing only eight PPR motifs, the other five proteins contain 18 PPR motifs and share high sequence similarity (93.595.3%) (Supplementary Data7). The rf4j, rf4b, rf4aus, and Rf4M proteins contain 782 amino acids, while rf4a has 798 amino acids (Supplementary Fig.3). In contrast to rf4j vs. Rf4M, which harbor 37 amino acids differences15,18, we detected 68 amino acid differences between rf4a and Rf4M, including two amino acid insertions at the N-terminal regions and 14 amino acid insertions at the C-terminal regions. In addition, rf4b has 38 amino acid differences, and rf4aus harbors 51 amino acid differences to Rf4M (Supplementary Fig.3). Compared to Rf4M, all rf4 proteins contain the common 14 amino acid substitutions at the PPR13, PPR14, and PPR15 motifs (Fig.3a and Supplementary Fig.3), suggesting that amino acid substitutions at these PPRs motifs are important for the fertility restoration of CMS-WA.

a Amino acid differences used to identify the functional Rf4 and non-functional rf4 variants in three PPR motifs (PPR13, PPR14, and PPR15). b Male fertility of transgenic (T0) lines of Jin23A (a CMS-WA line) carrying different transgenes (t) in the hemizygous state. For each complementary construct, at least 10 independent transgenic lines with similar phenotype were obtained. The pollen phenotype of three independent lines was shown in Fig.3b and Supplementary Fig.4. Viable pollen stain black; inviable pollen stain light brown. Scale bar: 50 m.

To verify our hypothesis that these rf4 variants may be non-functional for fertility restoration, binary vectors containing rf4a, rf4b, rf4j, rf4aus and Rf4M, all driven by the native promoter from Rf4, were constructed and introduced into the CMS-WA line Jin23A (WA352c/H4H4) via transformation. The male fertility of transgenic T0 plants with the transgene containing Rf4M was partially restored (Fig.3b and Supplementary Fig.4). Nevertheless, T0 transgenic plants carrying rf4a, rf4b, rf4j, or rf4aus remained completely sterile (Fig.3b and Supplementary Fig.4). These results confirm the notion that all the rf4 haplotypes are non-functional for fertility restoration of CMS-WA.

We demonstrated that the Rf4 locus has undergone CNV in different rice cultivars, and assumed that CNV at the Rf4 locus may be associated with the effect on fertility restoration of CMS-WA. To verify the CNV-mediated gene dosage effect of Rf4, we produced various lines with different copy numbers of Rf4 by crossing Jin23A (WA352c/H4H4) with two near-isogenic lines of Rf4: ZSRf4I (WA352c/H7H7) and ZSRf4M (WA352c/H1H1), knocking out Rf4 in ZSRf4M lines, and transforming Jin23A with functional Rf4, respectively (Figs.4, 5 and Supplementary Figs.5, 6). Firstly, the pollen viability (assessed by staining with I2KI) of the F1 plants derived from Jin23AZSRf4I (WA352c/H4H7) and Jin23AZSRf4M (WA352c/H4H1) were ~71% and ~88%, respectively, while the seed setting rates of these F1 plants were ~34% and ~52%, respectively (Fig.4a and Supplementary Figs.5a, 7a, b), showing the male fertility of the two-copy Rf4-carrying plants was higher than those of the one-copy Rf4-carrying plants (Fig.4 and Supplementary Figs.5, 7). Moreover, the fertile anthers were pollen-filled and yellowish, while the sterile anthers appeared thin and whitish (Figs.4, 5 and Supplementary Figs.5, 6).

a, b Pollen viability based on staining (upper panels), anther phenotype (middle panels), and seed setting rate (lower panels) of Jin23AZSRf4I (WA352c/H4H7), Jin23AZSRf4M (WA352c/H4H1) and rf4am-rf4bm-mF1/rf4am-rf4bm mutant lines (by CRISPR/Cas9 editing) in the ZSRf4M background. Red indicates the non-functional rf4a/bm after knockout of Rf4a/bM. Scale bars: 50 m in the upper panels, 1cm in the middle panels, and 5cm in the lower panels. ce Transcript levels of Rf4 (c) and WA352c (d, e) in different lines. UFC1 (UFM1-Conjugating Enzyme 1) and atp6 (a mitochondrial gene) served as internal references for Rf4 and WA352c expression, respectively. Data are shown as meanSD, n=3 biological replicates. Significant differences between two samples were determined by two-tailed Students t-test (**P<0.01, ***P<0.001, ****P<0.0001). f Sequencing of the Rf4a/bM-knockout plants derived from CRISPR/Cas9 editing. The underlined bases show protospacer adjacent motifs (PAMs). The positions highlighted in red indicate the targeted mutations. Source data are provided as a Source data file.

a Pollen staining (upper panels) to reveal viable pollen (dark), anther phenotype (middle panels) and seed setting rate (lower panels) of Jin23A/Rf4t- (WA352c/H4Rf4t-), Jin23A/Rf4tRf4t (WA352c/H4H4Rf4tRf4t), and Jin23A/Rf4tRf4tZSRf4I (WA352c/H4H7Rf4t-). Scale bars: 50 m in the upper panels, 1cm in the middle panels, and 5cm in the lower panels. b, c Transcript levels of Rf4 (b) and WA352c (c) in different lines. Rf4t indicates the Rf4 transgene, Rf4t- indicates transgenic hemizygotes. Data are shown as meanSD, n=3 biological replicates. Significant differences between two samples were determined by two-tailed Students t-test (**P<0.01, ***P<0.001, and NS represents No Significance). Source data are provided as a Source data file.

Furthermore, we knocked out both Rf4aM and Rf4bM in ZSRf4M line by CRISPR/Cas9 editing and obtained several rf4am and rf4bm mutants, which showed full abortion of pollen and spikelet (Fig.4b, Supplementary Fig.5b, and Supplementary Table2). Then, we selected three rf4am and rf4bm loss-of-function mutant lines (carrying different editing patterns) and crossed them with wild type ZSRf4M to test the dosage effect of Rf4 in the resultant mutant F1 (mF1) (Fig.4b and Supplementary Fig.5b). As expected, the pollen and spikelets of mF1 plants carrying two copies of Rf4 (WA352c/H1h1) also showed lower pollen viability (~85%) and seed setting rate (~48%), compared to those of wild type ZSRf4M (~92% and ~72%, respectively), which carries four copies of Rf4 (Fig.4b and Supplementary Figs.5b, 7c, d).

To clarify the connection between the Rf4 CNV-mediated gene dosage effect and the WA352c repression in fertility restoration, we performed qRT-PCR analysis of Rf4 and WA352c expression in anthers of different plants at the microspore mother cell stage. The expression level of Rf4 was twice as high in Jin23AZSRf4M (WA352c/ H4H1) vs. Jin23AZSRf4I (WA352c/H4H7) (Fig.4c and Supplementary Fig.5c), whereas the expression pattern of WA352c was opposite to that of Rf4 (Fig.4d and Supplementary Fig.5d). The level of WA352c transcripts was higher in the rf4am-rf4bm-mF1 and rf4am-rf4bm lines compared to ZSRf4M (Fig.4e and Supplementary Fig.5e).

In addition, we generated Rf4t-transgenic lines using CMS line Jin23A as recipient and selected a homozygous Jin23A/Rf4tRf4t (WA352c/H4H4Rf4tRf4t) plant from the T1 population to cross with ZSRf4I generating F1 plants Jin23A/Rf4tRf4tZSRf4I (WA352c/H4H7Rf4t-). We then acquired a series of materials harboring different copy numbers of the Rf4t transgene in the F2 population. As expected, lines with two-copy Rf4, including Jin23A/Rf4tRf4t (WA352c/H4H4Rf4tRf4t) and Jin23A/Rf4tRf4tZSRf4I (WA352c/H4H7Rf4t-), exhibited higher pollen viability (~87%, ~90%) and spikelet fertility (~52%, ~53%) than J23A/Rf4t- lines harboring a single copy of Rf4 (WA352c/H4H4Rf4t-), which showed ~73% pollen fertility and ~36% spikelet fertility (Fig.5a and Supplementary Figs.6a, 7e, f).

The level of Rf4 transcripts in Jin23A/Rf4tRf4t (WA352c/H4H4Rf4tRf4t) and Jin23A/Rf4tRf4tZSRf4I (WA352c/H4H7Rf4t-) was about twice as high as that in Jin23A/Rf4t- (WA352c/H4H4Rf4t-) in qRT-PCR assays (Fig.5b and Supplementary Fig.6). Consistent with this, the pattern of WA352c transcript levels was opposite to that of Rf4 (Fig.5c and Supplementary Fig.6c).

Together, these results supported the hypothesis that the dosage effect caused by different copy number of functional Rf4 plays an important role in fertility restoration of CMS-WA.

The ability to restore fertility of CMS lines restricts hybrid rice production; therefore, genetic resources with two-copy Rf4 might be beneficial for breeding stronger restorer lines for CMS-WA in hybrid rice production. To investigate the relationship between haplotypes of the Rf4 locus and the application of major restorer lines in China, we obtained data about the planting areas of hybrid rice varieties and crossing combinations of restorer lines for CMS-WA from the China Rice Data Center (https://www.ricedata.cn/). With regards to planting area of three-line hybrid rice cultivars, we selected the top sixteen related restorer lines for analysis: six lines (MH63, Ce64-7, CDR22, FuHui838, MH86, and ChengHui727) carried H1 (Rf4aM-Rf4bM), eight lines (MiYang46, Gui99, IR24, R402, Shuhui527, Huazhan, Guanghui998, and Minhui3301) harbored H7 (Rf4aI-rf4b), XianHui207 contained H8 (rf4a-Rf4bM), and MianHui725 possessed H6 (Rf4bM) (Supplementary Table3). As expected, hybrid rice varieties using six restorer lines carrying two-copy Rf4 (H1) had a larger total planting area (135,998,667 hectares) than the hybrid rice varieties using ten restorer lines having the one-copy Rf4 (78,015,332 hectares) (Fig.6). Notably, the two most widely planted hybrid rice varieties were bred from two elite restorer lines, MH63 and Ce64-7, both carrying the two-copy Rf4 (Supplementary Table3).

Total planting areas and relative percentage of hybrid rice varieties in China using 6 restorer lines carrying the two-copy Rf4 (H1) and 10 restorer lines with one-copy Rf4 (H6, H7, H8). The data information is given in Supplementary Table3.

The rice mitochondrial CMS-WA gene WA352c was generated in O. rufipogon via multiple rounds of recombination/protogene formation/functionalization, and WA352c has been widely utilized in hybrid rice breeding1. However, how WA352c co-evolved with Rf4 remains to be uncovered. To explore the evolutionary relationship of WA352c with Rf4, we analyzed their sequence structures in different O. rufipogon species and rice cultivars. The functional WA352c gene only coexisted with three haplotypes (H7, H14, and H28) of the Rf4 locus in O. rufipogon populations (Table1). This finding suggests that the first CMS-WA germplasm with abortive pollen discovered from an O. rufipogon population, called Wild Abortive, carrying a rf4a-like variant in addition to WA352c (Fig.7, Table1).

An Oryza rufipogon population (Wild Abortive) with the mitochondrial sterility gene WA352c and non-functional rf4a-like showing pollen abortion was found and used as the female parent for breeding CMS-WA lines by backcrossing with indica maintainer lines containing rf4i. A hybrid rice variety was bred by crossing the CMS-WA line with a restorer line (carrying one-copy or two-copy Rf4).

During the process of CMS-WA line breeding, the rf4a-like variant was replaced by rf4i through backcrossing with indica maintainer lines that harbor the rf4i variant, resulting in the current CMS-WA lines (Fig.7, Table1). CMS-WA (WA352c/rf4irf4i), maintainer (rf4i), and restorer lines (Rf4) made up the CMS-WA/Rf system for three-line hybrid rice production (Fig.7). Based on the above results and the previous finding that WA352c originates in O. rufipogon1, it appears that Rf4 and rf4 (except for rf4a and rf4aus) originated earlier than WA352c (Fig.7, Table1, and Supplementary Data3) and that the replacement of rf4i derived from indica type maintainer lines occurred during the creation of modern CMS-WA lines.

To facilitate the identification of Rf4 (rf4) haplotypes in hybrid rice breeding, we selected and optimized a set of eight Rf4 variant-specific PCR-based markers based on the SNPs at the Rf4 locus (Supplementary Table1). To confirm the utility of this set of markers, these primers were used to investigate the genotypes of 304 Asian cultivated rice germplasms. PCR products of these lines were first divided into three types, Copy-a, Copy-b, and Copy-a/-b, using two PCR markers (Copy-a-332 bp-F/R and Copy-b-282 bp-F/R), which generated 332-bp- and 282-bp PCR products from Copy-a and Copy-b, respectively (Fig.8 and Supplementary Table1). Then the variants and haplotypes of Rf4 and rf4 were determined using six specific primer sets. The fragments amplified from one-copy Rf4 from the Copy-a or Copy-b in rice varieties with the Rf4aI haplotype (such as Jalmagna and GH102) or Rf4bM haplotype (such as MH725 and R60) were 262bp long (Fig.8a). No products of functional Rf4 were amplified from japonica, indica, and aus varieties carrying haplotypes of rf4j, rf4i, and rf4aus, but a 372-bp, 358-bp, and 351-bp products of rf4 were obtained from the Copy-a of these varieties, respectively (Fig.8b).

Eight pairs of variant-specific primers were used for PCR to determine the Rf4 and rf4 haplotypes of different rice lines. a One-copy Rf4, b one-copy rf4, c two-copy Rf4. White dashed lines separate four different patterns of one-copy Rf4. GH993 (Guanghui993), XH207 (Xianhui207), ZSRf4I (Zhenshan Rf4I), IR8, Jalmagna, GH102 (Guanghui 102), MH725 (Mianhui725), R60, J23 (Jin23), ZS97 (Zhenshan97), IR64, 9311, MH63 (Minghui63), SH498 (Shuhui498), FH838 (Fuhui838), and IR30 are indica cultivars. Nip, T65, ZH11, and 9522 are japonica cultivars. CISOKAN, BaXiang, AR (Albania Rice), and ZCD13 (Zacaodao13) arecircum-aus cultivars. Actin1 was used as the PCR control. The PCR experiments for each sample were independently repeated at least three times with similar results. Source data are provided as a Source data file.

Varieties with the rf4a-Rf4bM haplotype (such as GH993 and XH207) or the Rf4aI-rf4b haplotype (such as ZSRf4I and IR8) all carried one-copy Rf4 (Fig.8a). They shared four common PCR products: Copy-a (332bp), Copy-b (282bp), Rf4 (262bp), and rf4a/b (197bp). Varieties with the rf4a-Rf4bM haplotype also generated another product: rf4a (446bp). Varieties carrying two-copy Rf4 with the Rf4aM-Rf4bM haplotype (such as MH63, SH498, FH838, and IR30) generated three PCR products: Rf4 (262bp), Copy-a (332bp), and Copy-b (282bp) (Fig.8c). Taken together, these results demonstrated that these primer sets are useful PCR markers for the rapid genotyping to accelerate the screening of strong restorer lines with the two-copy Rf4.

Go here to see the original:
Copy number variation of the restorer Rf4 underlies human selection ... - Nature.com

Media Highlights from Worlds First Whole Eye and Partial Face Transplant

Man Receives the First Eye Transplant Plus a New Face. Its a Step Toward One Day Restoring Sight This story was picked up by more than 200 local news outlets across the country. AP News November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Vaidehi S. Dedania, MD, associate professor, Department of Ophthalmology -Steven L. Galetta, MD, the Philip K. Moskowitz, MD Professor and Chair of Neurology, Department of Neurology, professor, Department of Ophthalmology

Man Who Narrowly Survived Electrical Accident Receives Worlds First Eye Transplant This story was picked syndicated across CBS News affiliates across the country. CBS News November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Vaidehi S. Dedania, MD, associate professor, Department of Ophthalmology

In a First, a Man Received a Whole Eye Transplant After Surviving High-Voltage Electric Shock NBC News November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Worlds First Whole-Eye and Partial Face Transplant Gives Arkansas Man New Hope CNN Health November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

NYU Langone Health Surgeon, Patient Show Off First-Ever Eye and Partial Face Transplant ABC7 November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

First Face-and-Eye Combo Transplant Makes History New York Post November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Samer Al-Homsi, MD, clinical professor, Department of Medicine, Division of Hematology and Medical Oncology, Perlmutter Cancer Center -Bruce E. Gelb, MD, associate professor, vice chair of quality, Department of Surgery, Division of Transplant Surgery

New York Surgeons Reveal Worlds First Eye Transplant (Subscription required.) The Wall Street Journal November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Vaidehi S. Dedania, MD, associate professor, Department of Ophthalmology

Surgeons in New York Announce Worlds First Eye Transplant Reuters November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

A High-Voltage Wire Destroyed His Face. Doctors Just Gave Him a New One. USA Today November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Bruce E. Gelb, MD, associate professor, vice chair of quality, Department of Surgery, Division of Transplant Surgery

The Worlds First Whole-Eye Transplant Is Helping an Arkansas Man Recover from Catastrophic Injury TIME November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Aaron James Lost Half His Face from Electrocution. He Just Received the First-Ever Eye and Face Transplant People November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Man Maimed by Electric Shock Receives First-Ever Face Transplant That Includes New Eye HealthDay November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Samer Al-Homsi, MD, clinical professor, Department of Medicine, Division of Hematology and Medical Oncology, Perlmutter Cancer Center -Bruce E. Gelb, MD, associate professor, vice chair of quality, Department of Surgery, Division of Transplant Surgery

Human Eyeball Successfully Transplanted for the First Time New Scientist November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Doctors Complete First Successful Face and Whole-Eye Transplant Scientific American November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Vaidehi S. Dedania, MD, associate professor, Department of Ophthalmology

U.S. Surgeons Perform Worlds First Whole Eye Transplant Yahoo! News November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Arkansas Man Receives Worlds First Whole-Eye, Partial Face Transplant (Subscription required.) Forbes November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Bruce E. Gelb, MD, associate professor, vice chair of quality, Department of Surgery, Division of Transplant Surgery

A Man Who Lost Half of His Face in a Work Accident Has Received the Worlds First Whole-Eye Transplant. He May Even See Out of It One Day. Insider November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

NYU Langone Health Performs the Worlds First Whole-Eye and Partial-Face Transplant for Military Veteran News Medical & Life Sciences November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery -Vaidehi S. Dedania, MD, associate professor, Department of Ophthalmology -Samer Al-Homsi, MD, clinical professor, Department of Medicine, Division of Hematology and Medical Oncology, Perlmutter Cancer Center -Bruce E. Gelb, MD, associate professor, vice chair of quality, Department of Surgery, Division of Transplant Surgery -Steven L. Galetta, MD, the Philip K. Moskowitz, MD Professor and Chair of Neurology, Department of Neurology, professor, Department of Ophthalmology

Surgeons Perform First-Ever Whole Eye and Partial Facial Transplant Inverse November 9 -Vaidehi S. Dedania, MD, associate professor, Department of Ophthalmology -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Doctors Successfully Performed the First Human Eyeball Transplant BroBible November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

This Man Received the First-Ever Whole-Eye Transplant Daily Beast November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Man Burned from the Inside Out in 7,200-Volt Electrocution Gets Worlds First Eye Transplant The Sun November 9 -Eduardo D. Rodriguez, MD, DDS, the Helen L. Kimmel Professor of Reconstructive Plastic Surgery, chair, the Hansjrg Wyss Department of Plastic Surgery

Man Who Had Entire Face Electrocuted Off at Work Looks Unrecognizable After Transplant Daily Star November 9 -NYU Langone Health

Half-Synthetic Yeast Engineered for the First Time Technology Networks November 8 -Jef D. Boeke, PhD, the Sol and Judith Bergstein Director, Institute of System Genetics, professor, Department of Biochemistry and Molecular Pharmacology

Fully Synthetic Genome Nears Completion in a Step Toward Unraveling Genetic Mysteries *Subscription required, please see full text at end of report. Endpoints News November 9 -Jef D. Boeke, PhD, the Sol and Judith Bergstein Director, Institute of System Genetics, professor, Department of Biochemistry and Molecular Pharmacology

NYU Langone Marks $2B in Donor Support Beckers Hospital Review November 8 -Robert I. Grossman, MD, dean and CEO, NYU Langone Health

Healthy Tissue May Predict Lung Cancer Return Better Than Tumors LiveScience November 8 -Aristotelis Tsirigos, PhD, professor, Department of Medicine, Division of Hematology and Medical Oncology, and Department of Pathology, Perlmutter Cancer Center

Male Patients, Black Patients, Rural Residents More Likely to Die of Pulmonary Embolism Healio November 8 -Shari B. Brosnahan, MD, assistant professor, Department of Medicine, Division of Pulmonary Medicine, Critical Care, and Sleep Medicine

The Most Common COVID Symptoms Doctors Are Seeing in Fall 2023 HuffPost November 9 -Sarah E. Hochman, MD, assistant professor, Department of Medicine, Division of Infectious Diseases & Immunology, section chief, Infectious Diseases, Tisch Hospital

What Can You Expect from a Stem Cell Transplant for PNH? HealthCentral November 8 -Mohammad Maher Abdul Hay, MD, associate professor, Department of Medicine, Division of Hematology and Medical Oncology, Perlmutter Cancer Center

Study Finds Higher B-Cell Levels in African American Patients with Multiple Sclerosis Managed Healthcare Executive November 8 -Haotian Xue, MD, resident physician, Department of Neurology, Multiple Sclerosis Comprehensive Care Center

Two Biomarkers Promising for Preeclampsia Prediction Medscape November 8 -Nieca Goldberg, MD, clinical associate professor, Department of Medicine, the Leon H. Charney Division of Cardiology

Why Everything About Weight Loss Changes After 35 Mens Health November 8 -Holly F. Lofton, MD, clinical associate professor, Departments of Surgery, Division of Bariatric Surgery, and Medicine, Division of General Internal Medicine

COVID Lockdowns Increased ADHD Risk Among 10-Year-Old Children Fox News November 9 -Marc K. Siegel, MD, clinical professor, Department of Medicine, Division of General Internal Medicine

Getting COVID and Flu Shots Together May Slightly Increase Risk of Stroke in Older Adults Health November 8 -Brandon Giglio, MD, clinical assistant professor, Department of Neurology, NYU Langone HospitalBrooklyn

* Endpoints News - November 9, 2023 - Fully Synthetic Genome Nears Completion in a Step Toward Unraveling Genetic Mysteries - An international effort to create yeast cells with a fully synthetic genome is nearing completion, with the eventual aim of unraveling the mysteries of genomes and ushering in a tool for producing complex medicines.

Scientists hope to create the synthetic organism by stitching together small pieces of DNA into artificial chromosomes and trimming out some genetic fat in the process.

The Synthetic Yeast Genome Project abbreviated Sc2.0 dates back more than 15 years. Now, in the consortiums biggest update since revealing five synthetic chromosomes in 2017, its scientists published 10 papers describing the creation of most of the remaining chromosomes, along with a wholly new one that does not exist in nature.

Weve got all 16 chromosomes completely synthesized, Jef Boeke, a synthetic biologist at NYU Langone Health and leader of the project, told Endpoints News. The group is still working on bringing those chromosomes, each in different yeast strains, together into a single organism. Were about a year or two away from completing that whole thing, Boeke said.

Scientists at the J. Craig Venter Institute, led by the eponymous geneticist who rose to fame as a leader of the Human Genome Project, have previously built viruses and bacteria from synthetic DNA. But the Sc2.0 yeast would be the most complex synthetic organism yet. And since yeast is more closely related to animals than bacteria, its a better stepping stone for answering questions about how human genomes work.

This is a gargantuan task, J. Craig Venter, whose institute was not involved in Sc2.0, said in an interview. Having a completely synthetic yeast would be a major milestone. I cant say how impressed I am with what theyve managed to pull off, he said.

Making a synthetic genome is not as simple as creating a carbon copy of what nature has already produced. The project is partly motivated by the belief that scientists can improve upon what nature has created.

These synthetic yeast cells allow us to think about how the genome could have been organized, Patrick Cai, a synthetic biologist at the University of Manchester, said in an email. Our understanding of genomes is largely based on the observation of these natural genomes. The ability to build synthetic genomes will lead us to a much deeper understanding of the first principles of life.

So far, the scientists have brought seven and a half synthetic chromosomes together under one Bakers yeast cell, accounting for 54% of the organisms DNA. That process of consolidation has proven trickier than expected, but scientists are already envisioning future uses for the completed cell.

Bakers yeast has always been the worlds number one microbe for making things for humans, said Tom Ellis, a synthetic biologist at Imperial College London whose lab constructed one of the yeast chromosomes. And with a finished synthetic cell, it opens up the possibility of making those products biochemicals, drugs, antibodies, vaccines, biomaterials in more optimal ways and with more diverse chemistry too.

Dreams of writing genomes, rather than just reading them, took hold at the turn of the century soon after scientists finished sequencing the first human genome. Researchers at Venters institute booted up the first bacteria with a synthetic genome in 2010 and refined and minimized its code in subsequent years.

For Boeke, creating a synthetic yeast genome was the natural next step. Yet, as simple as a yeast cell is compared to a human, its genome is still much larger than that of bacteria. It took about eight years before the first synthetic yeast chromosome was finished in 2014. In the years since, with the help of labs around the world and armies of undergrads, the Sc2.0 consortium has finally finished constructing the chromosomes.

One of the surprises that the group faced was that while the yeast was often healthy with one synthetic chromosome, the cells sometimes got sick when multiple synthetic chromosomes were added, sending the scientists back to the drawing board to figure out what went wrong and debug the design.

It indicates that there are more mysteries within the genomic sequences than we thought, said Junbiao Dai, deputy director of the Shenzhen Institute of Synthetic Biology, whose lab made one of the chromosomes. Debugging is a really big time-consuming process.

The Sc2.0 project shows that you have to build it to understand it, Venter said. Every time we or somebody else tries to make something, we find out that there are huge gaps in our knowledge.

The synthetic yeast genome has thousands of changes, reducing its length by about 10% compared to a natural genome, Boeke said. Some of those changes include stripping out repetitive DNA sequences that the scientists believe have accumulated over time and are unnecessary. So far, removing ones called transposons hasnt had a negative elect on the cells.

The team also did some reorganizing. Hundreds of genes encoding tRNA molecules which are crucial for protein production are normally scattered across the yeasts chromosomes. Cais lab took those genes and put them all together on a synthetic tRNA neochromosome.

Repetitive regions and tRNA genes are both hotspots for genetic mishaps that damage DNA. While clumping the tRNA genes together could really create a nightmare, some additional tinkering to reduce their liabilities seems to have worked, Boeke said. Were seeing if we can build a more stable genome than the natural genome.

They also installed tidbits of DNA throughout the genome that they can use to easily add, remove, or rearrange genes. That technique, called Scramble, allows scientists to rapidly generate thousands to millions of genetic variants of yeast. Boeke compares the approach to shuffling a massive deck of cards, each representing a gene, over and over.

One of those hands is going to give you a royal flush, the best possible hand in poker. And another ones going to give you the best hand in gin rummy, Boeke said, with different winning hands for researchers making antibodies, biofuels, or vaccine antigens. Its going to be a very practical tool for biotech companies that are trying to optimize yeast to produce useful products.

Its such a cool project, and coordinating all these institutions and investigators is a herculean task, said Jay Keasling, a bioengineer at the University of California, Berkeley, who was not involved in the e!ort. Its a stepping stone to what comes next, and just like DNA sequencing got cheaper and cheaper, doing this will get easier and easier.

Scientists are already envisioning a new project, Sc3.0, to dramatically shrink the size of the yeast genome, only retaining genes that are absolutely vital to life.

Imagine stripping back your smartphone to the most basic functions and having everything else as an optional app its battery life would probably be a lot better. Wed like to try to do that for cells, Ellis said.

Shen Yue, chief scientist of synthetic biology at BGI-Research in China, is excited to expand the genetic code of the synthetic yeast, allowing the cells to incorporate new amino acids beyond the standard twenty building blocks used to make peptides and proteins. Those new amino acids could grant new footholds for making antibody- drug conjugates, she said, or creating protein therapies with improved properties, like less frequent dosing.

Sc2.0 was once viewed as a stepping stone towards creating a fully synthetic human genome. Boeke was previously among the leaders of a grassroots effort called Human Genome Project-Write, announced in 2016. Yet, without concerted funding, the goal of synthesizing a human genome remains far off.

The human genome is 200 times larger, not to mention a lot more complicated and difficult to work with, Boeke said. Its just not practical.

Boeke said he withdrew from the group during the pandemic because his lab was busy helping with Covid-19 testing for New York City. But he also thinks that the time it would take to synthesize a full human genome poses a challenge. The cost of synthesizing DNA is another barrier.

Im surprised that the cost of the raw starting materials hasnt come down more, said Joel Bader, professor of biomedical engineering at Johns Hopkins University who was part of Sc2.0.

Several biotech companies are working on new methods for making DNA in the lab cheaper and faster. Its too soon to say if they will succeed, but the value of making fully synthetic genomes could soon be put to the test when the synthetic yeast is complete.

When all of those chromosomes are consolidated, thats when the power of Sc2.0 is really going to take off, Boeke said.

I have a bet on a case of very good wine with a colleague who thinks we wont be able to do it, he said. But Im pretty confident Im going to be drinking some good wine.

Originally posted here:
NYU Langone Health in the NewsThursday, November 9, 2023 - NYU Langone Health

Eugenics is the practice of breeding out diseases, unwanted characteristics and various disabilities. Early scientists wanted to take mental illness, poverty and criminal behavior out of the gene pool. This problematic gene science encouraged people with desirable traits to reproduce and people with undesirable traits to not have children. It is a form of scientific racism and ableism that plagues both the scientific community and general society, according to History.

The most common association with eugenics is Adolf Hitler and his concept of the so-called perfect Aryan race: blond-haired, blue-eyed and white. This instance of scientific racism is one of many instances of eugenics used throughout history and dates back to around 375 BCE Ancient Greece.

Eugenics means good creation, and one of the first mentions of eugenics was in Greek philosopher Platos The Republic. He wrote about a superior society where high-class people reproduce and discouraged anyone from procreating with lower-class people. In that same vein, he created a series of mating rules, such as men could only have arranged relationships by their ruler and promoted relationships between brothers and sisters.

One of the founding scientists of eugenics was Charles Darwins cousin Francis Galton. He hoped to make humankind better through procreating with the British elite. Instead, the concept became more popular in the United States.

The first instance of eugenics within Americas legislation was in 1896 when Connecticut made it illegal for feeble-minded people as well as people with epilepsy to marry. A few years later, in 1906, Americas Breeders Association was formed to study eugenics. This same association dealt with both animal and human genetic selection using Mendels Laws, according to the University of Washington Newspaper.

Kelloggs cereal creator, John Harvey Kellogg, created the Race Betterment Foundation in 1911 and established a pedigree registry to promote the concept of eugenics. This foundation and the Eugenics Records Office attempted to justify racism with fake science that said it caused flawed genes in minorities, immigrants and impoverished people.

From 1909 to 1979, California state mental institutions administered 20,000 sterilizations to stop people with mental illness people from having children. Later on, this would be done to minorities, which was legal in 33 states. During that time period, Hitler believed Germans should do whatever means necessary to eradicate non-Aryan races through genocide to make the gene pool stay pure. He was inspired by Americas eugenics laws, even going as far as to reference the countrys laws in his 1934 book, Mein Kampf, according to History.

Geneticist and co-founder of the double-helix James Watson has very racist beliefs when it comes to genetics and heavily believes in differences between the races. He attests that the differences in intelligence are because of race, still fundamentally believing Black people are not as smart as white people and upholding ideas of white supremacy, according to the New York Times.

Another surprising figure who promoted eugenics was Helen Keller. She was a blind and deaf activist and author but was a leading proponent of eugenics and the infanticide of disabled children. In her article in The New Republicin 1915, she calls disabled children a poor, misshapen, paralyzed, unthinking creature.

Keller was close friends with Alexander Graham Bell, a leading eugenist, who reportedly heavily influenced her views. Despite their friendship, he advocated for the sterilization of people he considered defective, including deaf people. Bell believed deaf people should not be allowed to marry, which makes their relationship contradictory and confusing, according to Autism Spectrum News.

Kellers views are very surprising because of the ableism and problematic ideas she and Bell perpetuated. She supported killing disabled children like herself while also advocating for the communitys rights. It is incredibly contradictory and upsetting, especially considering she was a member of the National Association for the Advancement of Colored People (NAACP). Eugenics has many racist as well as ableist implications.

Eugenics is an incredibly scary genetic science with a dark history that spans centuries. With a past ranging from Helen Kellers advocacy for the sterilization of disabled individuals to John Harvey Kelloggs fake science promoting racism, there are still lasting effects within science and societal institutions as a whole.

Originally posted here:
Eugenics: Plaguing scientific community with dark history | Opinion ... - The Arkansas Traveler