Cytoplasmic Type Research Articles

Cytoplasmic Types of Indian Potato Cultivars and Their Effect on Important Agronomic Traits

Cytoplasmic Types of Indian Potato Cultivars and Their Effect on Important Agronomic Traits

Elucidating Mitochondrial DNA Markers of Ogura-Based CMS Lines in Indian Cauliflowers (Brassica oleracea var. botrytis L.) and Their Floral Abnormalities Due to Diversity in Cytonuclear Interactions.

Mitochondrial markers can be used to differentiate diverse mitotypes as well as cytoplasms in angiosperms. In cauliflower, cultivation of hybrids is pivotal in remunerative agriculture and cytoplasmic male sterile lines constitute an important component of the hybrid breeding. In diversifying the source of male sterility, it is essential to appropriately differentiate among the available male sterile cytoplasms in cauliflower. PCR polymorphism at the key mitochondrial genes associated with male sterility will be instrumental in analyzing, molecular characterization, and development of mitotype-specific markers for differentiation of different cytoplasmic sources. Presence of auto- and alloplasmic cytonuclear combinations result in complex floral abnormalities. In this context, the present investigation highlighted the utility of organelle genome-based markers in distinguishing cytoplasm types in Indian cauliflowers and unveils the epistatic effects of the cytonuclear interactions influencing floral phenotypes. In PCR-based analysis using a set of primers targeted to orf-138, 76 Indian cauliflower lines depicted the presence of Ogura cytoplasm albeit the amplicons generated exhibited polymorphism within the ofr-138 sequence. The polymorphic fragments were found to be spanning over 200–280 bp and 410–470 bp genomic regions of BnTR4 and orf125, respectively. Sequence analysis revealed that such cytoplasmic genetic variations could be attributed to single nucleotide polymorphisms and insertion or deletions of 31/51 nucleotides. The cytoplasmic effects on varying nuclear-genetic backgrounds rendered an array of floral abnormalities like reduction in flower size, fused flowers, splitted style with the exposed ovule, absence of nonfunctional stamens, and petaloid stamens. These floral malformations caused dysplasia of flower structure affecting female fertility with inefficient nectar production. The finding provides an important reference to ameliorate understanding of mechanism of cytonuclear interactions in floral organ development in Brassicas. The study paves the way for unraveling developmental biology of CMS phenotypes in eukaryotic organisms and intergenomic conflict in plant speciation.

Nomenclatural standards and genetic passports of potato cultivars bred by the Tatar Research Institute of Agriculture «Kazan Scientific Center of the Russian Academy of Sciences»

Breeding of potato cultivars adapted to the climatic conditions of the Middle Volga region and resistant to various harmful organisms has always been an urgent task for breeders of the Tatarstan Republic. In the present paper, the potato cultivars bred at the Tatar Research Institute of Agriculture – Kazan Scientific Center of the Russian Academy of Sciences, were taken as an example for demonstrating the results of application and elaboration of methodological approaches that are currently developed at the N.I. Vavilov Institute of Plant Genetic Resources (VIR) for the preparing of nomenclatural standards and their genotyping. At the initiative of the VIR researchers in collaboration with the authors of potato cultivars E.A. Gimaeva and Z. Stashevski plant material was collected and nomenclatural standards for potato cultivars bred at the Kazan Scientific Center of the Russian Academy of Sciences were prepared. Four nomenclatural standards for Tatarstan potato cultivars (‘Zumba’, ‘Kortni’, ‘Reggi’, ‘Samba’) were prepared in accordance with the provisions of the International Code of Nomenclature For Cultivated Plants, registered in the VIR Herbarium Database, and transferred to the VIR herbarium type collection. Besides, voucher specimens of cv. ‘Tango’ and breeding clone ‘Sal’sa’, which is undergoing the State Variety Test at present, were produced. Genetic passports of Tatarstan varieties (‘Zumba’, ‘Kortni’, ‘Reggi’, ‘Samba’) and one breeding clone (‘Sal’sa’)* were developed using DNA samples from plant material transferred by the authors of the cultivars to the VIR herbarium. The genetic passports include information of the polymorphism of eight chromosome-specific microsatellites, data on the presence/ absence of the diagnostic fragments of 15 markers of the 11 R-genes conferring resistance to various harmful organisms and the information about cytoplasm types. A comparison of the data from genetic passports developed using DNA samples from nomenclatural standard specimens with the results of genotyping of 22 samples of Tatarstan cultivars obtained from different sources (e.g., samples undergoing ecogeographic tests within the framework of the Comprehensive Research Plan of the subprogram “Development of potato breeding and seed production in the Russian Federation”; as well as accessions from the VIR in vitro collection) made it possible to assess the authenticity and uniformity of the studied plant material.

Nomenclatural standards and genetic passports of potato cultivars bred at the Leningrad Research Institute for Agriculture “Belogorka”

In the present paper, the potato cultivars bred at the Leningrad Research Institute for Agriculture “Belogorka”, were taken as an example for demonstrating the results of elaboration of methodological approaches that are currently developed at the N.I. Vavilov Institute of Plant Genetic Resources (VIR) for the preparing of nomenclatural standards and their genotyping. In 2018, joint research of VIR scientists and breeders from the Leningrad Research Institute for Agriculture “Belogorka” began in the field of preparing nomenclatural standards for potato cultivars bred at this institute. Nomenclatural standards were prepared according to the ‘International Code of Nomenclature for Cultivated Plants’. Plant material for herbarium specimens was collected in the experimental field of the “Belogorka” Institute in 2018 by cultivar authors and handed over to the VIR Herbarium of cultivated plants, their wild relatives and weeds (WIR). The plant material included stems with inflorescences and later - tubers of 21 cultivars which were bred at the “Belogorka” Institute. Two precultivars undergoing State variety testing and three breeding clones were also included in this study. Just before herbarium preparation, the obtained plant material was photographed, plant morphological characters described, and the results compared with the description given in such official documents as the “Cultivar Questionnaireˮ and “Description of selection achievementˮ. The nomenclatural standards of 21 cultivars registered in the VIR Herbarium Database and transferred for conservation to the VIR herbarium, are published in this paper. Before herbarium preparation, the plant material was sampled for DNA extraction and subsequent genotyping and molecular screening. The genetic passports include information about the polymorphism of 10 chromosome-specific microsatellite loci, as well as the data on the presence/absence of diagnostic fragments of 12 markers of the 11R-genes conferring resistance to diseases and pests, and for some cultivars – the information about their cytoplasm type. These genetic passports are valuable not only because different types of DNA markers were used in their preparing (SSR, SCAR and CAPS markers of theRgenes; markers specific to different loci of the nuclear and organelle genomes), but first of all because of the material itself, as the DNA samples were isolated from the plants with the assigned status of nomenclatural standard for each particular cultivar. Based on the genetic passports data, trueness to type of the “Belogorka” cultivar samples obtained from various sources was verified.

Abstract PO-029: USP14 is a potential target to improve the efficacy of radiotherapy in combination with immune-checkpoint inhibitors in non-small cell lung cancer

Abstract Non-small cell lung cancer (NSCLC) represents ~85% of lung cancer cases and has a 5-year survival rate of ~23%. Thus, research aimed at determining more effective treatment strategies is critical. Immune checkpoint inhibitors (ICis), e.g. anti-PD-L1 antibodies, have transformed cancer treatment in recent years. Clinical trial studies have indicated that radiotherapy enhances the curative effect of ICis. However, most patients do not respond to immune-radiotherapy combinations. While best known to induce DNA double strand break (DSB)-mediated cytotoxicity, ionizing radiation (IR) induces an increase of cytosolic DNA and activates the cyclic GMP-AMP synthase/stimulator of interferon genes (cGAS/STING) signaling pathway that leads to the type 1 interferon (IFN) response, essential to achieve anti-tumor immunity in combination with ICis. Homologous recombination (HR) DNA repair deficiency is an important determinant of radiation response that can also increase the immune recognition of cancers by increasing the number of non-synonymous mutations, as well as by increasing the cGAS/STING-mediated type1 IFN response. We have shown an important role for ubiquitin specific protease (USP14) in regulating DNA repair (1, 2,3). Here, we identify a novel role of USP14 in regulating HR and the cGAS/STING pathway in response to IR in NSCLC. USP14 is a proteasomal deubiquitinase that we show to have a prominent role in NSCLC. Knockdown of USP14 (shUSP14) or its pharmacological inhibition (IU1 or VLX1570) led to: (i) radio-sensitization, as shown by reduced clonogenic survival in NSCLC cell lines, and delayed growth of NSCLC tumor xenografts in nude mice; increased (ii) HR-deficiency; (iii) chromosomal aberrations and micronuclei formation; as well as (iv) cGAS puncta in response to IR. Further, USP14 interacts with and deubiquitinates cGAS in IR-treated NSCLC cells. USP14-mediated deubiquitination of cGAS has been shown to inhibit cGAS protein turn-over and increase the levels of cGAS in response to virus infection. Unexpectedly, however, in response to IR shUSP14 NSCLC cells have significantly higher cytoplasmic cGAS puncta and type 1 IFN response. Overall, these findings identify USP14 as a potential target to enhance sensitization to immune-radiotherapy by both regulation of HR and direct regulation of cGAS ubiquitination, leading to type 1 IFN response. Understanding the mechanisms that regulate DSB repair and cGAS/STING pathways holds potential for developing strategies to enhance the effectiveness of immune-radiotherapy combinations in NSCLC.

Interspecific crosses involving Rf3 gene carriers as potential sources of R lines for D2 type cytoplasm based hybrid wheat system

The exploitation of heterosis, which is associated with the development of hybrid wheat varieties, has a great potential for increasing global wheat grain yields. Nevertheless, common wheat hybrids now account for less than 1% of global wheat production. In practice, two general approaches in hybrid wheat seeds production are being used. The first is based on the application of a chemical hybridizing agent, while the second is based on the use of cytoplasmic-genetic male sterility derived from Triticum timopheevii Zhuk. (G type cytoplasm). In this study, we present the development of R (restorer) lines for an alternative hybrid wheat system based on the cytoplasm of Aegilops crassa Boiss. (D2 type cytoplasm). Considering the cytoplasm types, it was found that different types of experimental F1 crosses required different sources of fertility restorer genes. CMS materials with T. timopheevii cytoplasm achieved the highest productivity in combination with Rf3 gene carriers. On the other hand, CMS materials with D2 cytoplasm in combination with interspecific crosses of synthetic hexaploid wheat accessions and SBEII mutants led to highly heterotic F1 hybrids. D2 cytoplasm based male sterility induction system represents a promising tool for hybrid wheat development.

Cytoplasmic genome of Indian potato varieties and breeding lines vis a vis prospects in potato breeding

Advances in research resulted in development of a simple, rapid and reliable multiplex PCR protocol for cytoplasm differentiation in potato. Applying this rapid technique, we assessed the cytoplasm diversity in 57 Indian potato varieties, 15 popular exotic varieties and 47 biotic stress resistance breeding parental lines using five DNA based markers. Results revealed that T is the predominant cytoplasm type followed by D in Indian and exotic potato varieties as well as parental lines. The proportion of T and D type cytoplasm was 77.2% and 19.3% and 73.3% and 20.0% in Indian and exotic varieties, respectively. A and W type were found in one variety each, while M and P were missing in Indian varieties. All the popular Indian table potato varieties have tuberosum type cytoplasm with few exceptions of varieties bred for biotic stress resistance namely Kufri Himalini, Kufri Girdhari, carrying demissum cytoplasm. Opposite was true for Indian processing cultivars with the exception of Kufri Chipsona 4, which had T type cytoplasm. Evaluation of biotic stress resistance breeding parental lines showed increasing use of D (34.0%) and W (12.8%) cytoplasm in comparison to previously bred varieties. Although D type cytoplasm is associated with late blight resistance and male sterility, all Indian cultivars with D type cytoplasm are not resistant to late blight, nor they all are male sterile. Male fertile D type cytoplasm and the cytoplasms showing good interaction between cytoplasmic and nuclear gene for agronomic traits should be incorporated in the parental lines. Efforts must also be done to diversify the cytoplasm of cultivated potato with at least semi-cultivated cytoplasm types.

Nuclear and chloroplast genome diversity revealed by low-coverage whole-genome shotgun sequence in 44 Brassica oleracea breeding lines

Whole-genome shogun sequence (WGS) data generated by next-generation sequencing (NGS) platforms are a valuable resource for crop improvement. We produced 5–6 × WGS coverage of 44 Brassica oleracea breeding lines representing seven subspecies/morphotypes: cabbage, broccoli, cauliflower, kailan, kale, Brussels sprout, and kohlrabi to systematically evaluate the nuclear and chloroplast (Cp) diversity in the 44 B. oleracea breeding lines. We then exploited the impact of low-coverage NGS by evaluating nuclear genome diversity and assembly, annotation of complete chloroplast (Cp) genomes and 45S nuclear ribosomal DNA (45S nrDNA) sequences, and copy number variation for major repeats. Nuclear genome diversity analysis has revealed a total of 496 463 SNPs and 37 493 indels in the nuclear genome across the 44 accessions. Interestingly, some SNPs showed subspecies enrichment at certain chromosomal regions. The assembly of complete Cp genomes contained 153 361–153 372 bp with 37 variants including SNPs and indels. The 45S nrDNA transcription unit was 5 802 bp long with a total of 31 SNPs from the 44 lines. The phylogenetic tree inferred from the nuclear and Cp genomes coincided and clustered broccoli, cauliflower, and kailan in one group and cabbage, Brussels sprout, kale, and kohlrabi in another group. The morphotypes diverged during the last 0.17 million years. The Cp genome diversity reflected the unique cytoplasm of each subspecies, and revealed that the cytoplasm of many breeding lines was replaced and intermingled via inter-subspecies crosses during the breeding process instead. The polymorphic Cp markers provide a classification system for the cytoplasm types in B. oleracea. Furthermore, copy numbers of major transposable elements (TEs) showed high diversity among the 44 accessions, indicating that many TEs have become active recently. Overall, we demonstrated a comprehensive utilization of low-coverage NGS data and might shed light on the genetic diversity and evolution of diverse B. oleracea morphotypes.

Analysis of the Composition of Fertility Genes in Sterile and Maintainer Lines of Sugar Beet

This study attempted to characterize the cytoplasmic types of three sterile lines and three maintainer lines of sugar beet, as well as the composition of the Rf1 and Rf2 fertility genes, utilizing molecular markers. Male sterile cytoplasm (S) and normal cytoplasm (N) in sugar beet were identified by polymorphisms in the variable number of tandem repeats (VNTR) locus. Molecular markers s17 and o7 were used to identify the composition of Rf1 and Rf2 fertility genes. In addition, the other four pairs of primers (4E2M15S, 5E3M5S, 1E8M7O and 11E8M4S), which were designed on the basis of genomic and transcriptomic sequences, were selected to identify male sterile and maintainer lines. The amplification bands of VNTR primers demonstrated that the cytoplasmic type of maintainer and sterile lines was N-type and S-type, respectively. The observed segregation of s17 did not significantly difference (p = 1) among three maintainer lines, while significant difference (p < 0.01) was found among three sterile lines. Among four pairs of genomic and transcriptomic primers, only 11E8M4S was observed to distinguish between sterile and maintainer lines of sugar beet. In conclusion, VNTR primers have a high accuracy for identifying the cytoplasmic type of maintainer and sterile lines. s17 and 11E8M4S were also effective for DNA marker-assisted selection of sterile and maintainer lines in sugar beet. However, o7 was not significantly correlated with the fertility of sterile and maintainer lines, suggesting that the Rf2 site may play a little role in the restored fertility of sugar beet.

Russian-language adaptation of the international nomenclature of International Consensus on Antinuclear Antibody (ANA) Patterns (ICAP)

Antinuclear antibodies (ANAs) represent a spectrum of autoantibodies targeted for various nuclear and cytoplasmic components of the cells. Indirect immunofluorescence assay (IIF) is the main detection method for “antinuclear factor”. A positive ANA test is usually reported as a titer and a pattern of fluorescence. The ANA patterns refers to the distribution of staining produced by antibodies that react with antigens located in nucleus and cytoplasm of HEp-2 cells. To standardize nomenclature and descriptions of the various fluorescence patterns of antinuclear factor (ANF), the Initiative of the International Consensus on ANA Patterns (ICAP) group was developed in 2014. The aim of ICAP is to promote consensus regarding nomenclature of ANA patterns, a microphotograph database, as well as classification depending on the employee skills. Information on the main characteristics, as well as specific clinical associations of the patterns is available at www.ANApatterns.org. In ANA classification trees, the patterns are indicated by the #AC (anticell pattern) alphanumeric code, being divided into nuclear, cytoplasmic and mitotic groups. Depending on the clinical significance and/or ease of recognition, this nomenclature focuses on the differences between the patterns described by specialists at competent and expert levels. Of the nuclear types, the most significant are homogeneous, speckled, dense fine-speckled, centromere, nucleolar, nuclear dots. The cytoplasmic types may be discerned into fibrillar, speckled, mitochondrial, Golgi, rods and rings. On leaders, behalf of the ICAP translation team is headed by the Full Member of Russian Academy of Sciences, Professor A.A. Totolian, under the auspices of the Russian Research Society of Immunologists. In this article, we present the Russianlanguage adaptation of the ICAP nomenclature, in order to ensure unification and standardization of ANA detection results in the patients with autoimmune diseases.

Combinational ability of crossing components and heterosis of F1 hybrids of sugar sorghum by biomass yield

Currently, the most promising direction of breeding is the creation of F1 hybrids of sugar sorghum, based on the identification and selection of parental forms with high combinational ability. The source material and F1 hybrids were grown in the arid conditions of the Saratov Right Bank (Russia): the hydrothermal coefficient during the growing season was 0.68. The evaluation of the combinational ability of crossing components was carried out using the topcross method. As a result of the tests, the L-52/13 line was identified with high GCA effects (15.71), and the highest SCA dispersions were found in the Saratovskoe 90 variety and the L-39/12 line (91.80-189.27). It was found that the type of sterile cytoplasm of iso-nuclear CMS-lines had a significant impact on the manifestation of SCA in terms of biomass yield: higher dispersion indicators were noted in 9E Zheltozernoye 10 (36.66). Genes with an additive effect are involved in the genetic control of this trait in paternal forms, and non-additive genes in maternal forms. In addition, each hybrid combinationwas observed with superdomination: the coefficient of phenotypic dominance varied from 2.01 to 18.91. It is advisable to use the obtained information in the hybridization of sugar sorghum to obtain high-heterosis hybrids.

Necrotising Cutaneous Lesions in Anti Neutrophil Cytoplasmic Antibodies- Associated Vasculitis Mimicking Necrotising Fasciitis

Necrotising vasculitis is a very rare occurrence and commonly caused by an underlying autoimmune pathology. Anti Neutrophil Cytoplasmic Antibodies (ANCA) associated vasculitis is an established cause for cutaneous manifestations of necrotising vasculitis, and is associated with multisystemic involvement, in which presentations of one system may feature predominantly and lead to misdiagnosis. A 33-year-old male presented with acute history of shortness of breath and necrotising blisters over both his ankles and arms. He was initially provisionally diagnosed with necrotising fasciitis, which was eventually ruled out as the serological biomarkers (including low level of C3 and presence of cytoplasmic type of ANCA on indirect immunofluorescence) drew suspicion of an autoimmune pathology. A multidisciplinary approach led to the commencement of steroid, which improved the patient’s condition rapidly. The histological examination of sample from the skin biopsy later confirmed the diagnosis of ANCA-Associated Vasculitis (AAV). The patient eventually recovered with excellent outcomes. Despite its rarity, any abnormal skin lesion may be a subtle presentation of necrotising cutaneous vasculitis. A high index of suspicion through a multidisciplinary approach, coupled with meticulous investigative process including serological biomarkers and skin biopsy, helps to avoid misdiagnosis which may be detrimental to the patient.

Paraneoplastic Myeloneuropathies: Clinical, Oncologic, and Serologic Accompaniments.

ObjectiveTo test the hypothesis that myeloneuropathy is a presenting phenotype of paraneoplastic neurologic syndromes we retrospectively reviewed clinical, radiologic, and serologic features of 32 patients with concomitant paraneoplastic spinal cord and peripheral nervous system involvement.MethodsObservational study investigating patients with myeloneuropathy and underlying cancer or onconeural antibody seropositivity.ResultsAmong 32 patients with paraneoplastic myeloneuropathy, 20 (63%) were women with median age 61 years (range 27–84 years). Twenty-six patients (81%) had classified onconeural antibodies (amphiphysin, n = 8; antineuronal nuclear antibody [ANNA] type 1 [anti-Hu], n = 5; collapsin response mediator protein 5 [CRMP5] [anti-CV2], n = 6; Purkinje cell cytoplasmic antibody type 1 [PCA1] [anti-Yo], n = 1; Purkinje cell cytoplasmic antibody type 2 [PCA2], n = 2; kelch-like protein 11 [KLHL11], n = 1; and combinations thereof: ANNA1/CRMP5, n = 1; ANNA1/amphiphysin, n = 1; ANNA3/CRMP5, n = 1). Cancer was confirmed in 25 cases (onconeural antibodies, n = 19; unclassified antibodies, n = 3; no antibodies, n = 3). Paraneoplastic myeloneuropathies had asymmetric paresthesias (84%), neuropathic pain (78%), subacute onset (72%), sensory ataxia (69%), bladder dysfunction (69%), and unintentional weight loss >15 pounds (63%). Neurologic examination demonstrated concomitant distal or asymmetric hyporeflexia and hyperreflexia (81%), impaired vibration and proprioception (69%), Babinski response (68%), and asymmetric weakness (66%). MRI showed longitudinally extensive (45%), tract-specific spinal cord T2 hyperintensities (39%) and lumbar nerve root enhancement (38%). Ten of 28 (36%) were unable to ambulate independently at last follow-up (median 24 months, range 5–133 months). Combined oncologic and immunologic therapy had more favorable modified Rankin Scale scores at post-treatment follow-up compared to those receiving either oncologic or immunologic therapy alone (2 [range 1–4] vs 4 [range 2–6], p < 0.001).ConclusionsParaneoplastic etiologies should be considered in the evaluation of subacute myeloneuropathies. Recognition of key characteristics of paraneoplastic myeloneuropathy may facilitate early tumor diagnosis and initiation of immunosuppressive treatment.

Myelitis Presenting Anti-Yo Antibody in a Patient with Prostatic Adenocarcinoma

Antineuronal antibody-associated paraneoplastic neurologic syndromes result from tumor-stimulated autoimmune attacks against components of the nervous system. Paraneoplastic myelopathy associated with Purkinje-cell cytoplasmic autoantibody type 1 (anti-Yo) is extremely rare disorder. It is almost exclusively reported in women with gynecological tumors. Even though few cases of anti-Yo-associated paraneoplastic neurologic syndrome related to other cancers are reported, it is a very uncommon condition, especially in males. The author report here the first case of anti-Yo myelopathy with prostatic adenocarcinoma.

Influence of different types of sterile cytoplasms (A3, A4, 9E) on the combining ability of CMS lines of sorghum.

Investigation of the effect of the cytoplasm on the combining ability (CA) of lines with cytoplasmic male sterility (CMS) is of considerable interest in terms of understanding the genetic functions of the cytoplasm and for practical purposes to create hybrids with improved economically valuable traits. In order to investigate the effect of different types of sterile cytoplasm (A3, A4, 9E) on CA in sorghum, we studied the manifestation of a number of biological and agronomic traits in 54 F1 hybrid combinations obtained using iso-nuclear CMS lines with the nuclear genome of the line Zheltozernoye 10, differing only in the types of sterile cytoplasm (A3, A4 and 9E). Eighteen varieties and lines of grain sorghum developed at the Russian Research and Project-technological Institute of Sorghum and Maize were used as paternal parents. The CA was determined by the topcross method. F1 hybrids and their parents were grown in 2015–2017 in conditions of insufficient (2015–2016: HTC (hydro-thermal coefficient) = 0.32–0.66), or good water availability conditions (2017: HTC = 1.00). On average, for three years of testing, a positive effect of the 9E cytoplasm on the general combining ability (GCA) (0.63) and negative effects of the A3 and A4 cytoplasms (–0.32 and –0.31) for the inflorescence length were noted. In dry seasons, significant positive effects of the 9E cytoplasm on GCA for the length of the largest leaf, and positive effects of the A3 cytoplasm on GCA for the plant height, and negative effects of the A4 cytoplasm on GCA for these traits were observed. No differences were observed during the wet season. The type of CMS did not affect the GCA for the width of the largest leaf and grain yield. The dispersion of specific combining ability (SCA) in the dry seasons was significant for the following traits: leaf length, plant height, panicle length and width, and grain yield, the 9E cytoplasm had the highest SCA dispersion, whereas the A4 cytoplasm had the smallest one. The data obtained indicate that different types of sterile cytoplasm of sorghum make a different contribution to CA under conditions of drought stress.

Muscle biopsy in anti-neutrophil cytoplasmic antibody-associated vasculitis: diagnostic yield depends on anti-neutrophil cytoplasmic antibody type, sex and neutrophil count.

This study aimed to examine the sensitivity of muscle biopsy (MB) in ANCA-associated vasculitis (AAV), identify factors predicting MB positivity and assess the prognostic value of a positive MB. We conducted a single-centre retrospective study of AAV with an MB performed at diagnosis. AAV classification [granulomatosis with polyangiitis (GPA), microscopic polyangiitis (MPA), eosinophilic granulomatosis with polyangiitis (EGPA)] followed the European Medicines Agency algorithm. A logistic regression model was used to identify the factors associated with MB positivity. Survival curves were generated using the Kaplan-Meier method. Among 276 AAV patients (1995-2018), 101 had an MB. Seventy-eight patients were included: 33 with GPA, 25 with MPA and 20 with EGPA. MB samples were positive in 45 cases (58%): 17 GPA, 16 MPA and 12 EGPA. Univariate analysis focussed on GPA and MPA, revealed that the MB yield was higher in females [22/31 (71%) vs 11/27 (41%); P = 0.02] and in anti-MPO patients [25/37 (68%) vs 6/19 (32%) for anti-PR3; P = 0.01]. By multivariate analysis, three factors predicted MB positivity: anti-MPO ANCA [odds ratio (OR) 10.67 (CI 2.09, 81.68)], female sex [OR 5.3 (CI 1.16, 32.35)] and neutrophil count [OR 1.33 (CI 1.07, 1.8)]. MB positivity had no impact on relapse, death or end-stage renal disease-free survival. MB is a safe and efficient diagnostic tool for AAV. Predictors of MB yield include ANCA type, sex and neutrophil count. MB cannot substitute for kidney biopsy when indicated, but should be considered in other cases.

EXPRESSION OF CD10 IN CARCINOMA PROSTATE AND ITS CORRELATION WITH VARIOUS CLINICOPATHOLOGICAL PARAMETERS.

Aim: Adenocarcinoma of the prostate is the second most common cause of cancer. Loss of CD10 is a common early event in human prostate cancer and is seen in lower Gleason Score malignancies while increased and altered expression is seen in high Gleason Score tumors, lymph node and bone metastasis. Materials and methods: The present study was a prospective observational study conducted on seventy-five patients suspected of having prostate cancer. Immunohistochemical profile was assessed for PSA, AMACR and CD10 immunostain. The intensity of CD10 expression and pattern of CD10 staining of tumor cells was evaluated. Results: The patients were in age group of 50-90 years with a mean age of 70.97 ± 9.51 years. As the grade group/gleason score increased the number of cases showing negative expression decreased and the pattern of expression changed from membranous to cytoplasmic to both types of expression. As the serum PSA levels increased the intensity of expression changed from focally positive to diffusely positive. The pattern of expression also changed from membranous to cytoplasmic to both ( membranous + cytoplasmic ) types of expression with increase in PSA levels. Conclusion: By immunohistochemical analysis we can identify CD10 positive tumors, which may warrant more aggressive initial therapy. A number of drugs against CD10 are available based on which potential targeted therapies could be formulated.

Multicentric origin and diversification of atp6-orf79-like structures reveal mitochondrial gene flows in Oryza rufipogon and Oryza sativa.

Cytoplasmic male sterility (CMS) is a widely used genetic tool in modern hybrid rice breeding. Most genes conferring rice gametophytic CMS are homologous to orf79 and co‐transcribe with atp6. However, the origin, differentiation and flow of these mitochondrial genes in wild and cultivated rice species remain unclear. In this study, we performed de novo assembly of the mitochondrial genomes of 221 common wild rice (Oryza rufipogon Griff.) and 369 Asian cultivated rice (Oryza sativa L.) accessions, and identified 16 haplotypes of atp6‐orf79‐like structures and 11 orf79 alleles. These homologous structures were classified into 4 distinct groups (AO‐I, AO‐II, AO‐III and AO‐IV), all of which were observed in O. rufipogon but only AO‐I was detected in O. sativa, causing a decrease in the frequency of atp6‐orf79‐like structures from 19.9% to 8.1%. Phylogenetic and biogeographic analyses revealed that the different groups of these gametophytic CMS‐related genes in O. rufipogon evolved in a multicentric pattern. The geographical origin of the atp6‐orf79‐like structures was further traced back, and a candidate region in north‐east of Gangetic Plain on the Indian Peninsula (South Asia) was identified as the origin centre of AO‐I. The orf79 alleles were detected in all three cytoplasmic types (Or‐CT0, Or‐CT1 and Or‐CT2) of O. rufipogon, but only two alleles (orf79a and orf79b) were observed in Or‐CT0 type of O. sativa, while no orf79 allele was found in other types of O. sativa. Our results also revealed that the orf79 alleles in cultivated rice originated from the wild rice population in South and South‐East Asia. In addition, strong positive selection pressure was detected on the sequence variations of orf79 alleles, and a special evolutionary strategy was noted in these gametophytic CMS‐related genes, suggesting that their divergence could be beneficial to their survival in evolution.

Paraneoplastic ataxic syndrome with anti-Yo antibodies in breast and ovarian cancer: A retrospective analysis.

e18089 Background: Paraneoplastic cerebellar syndrome is a rare immunological reaction caused most commonly by Anti-Yo or Purkinje cell cytoplasmic antibody type 1(PCA1) to cerebellar degeneration protein 2(CDR2), found in the cerebellum and ectopically produced by tumor. Most cases are reported in women with HER2+ breast and ovarian cancers with underlying breast cancer patients having relatively better prognosis. Treatment initiation within one month of symptom onset has shown better outcomes. Methods: A retrospective analysis was conducted using a clinical database at a single institution and included 3 patients with a cancer diagnosis and ataxic symptoms diagnosed between 2016 and 2020. Data collection included age, gender, performance status, site of disease, pathology, diagnostic work up, treatment and overall survival (OS). Results: The study included 3 patients who presented with new onset ataxic symptoms with the median time of cancer diagnosis from onset of symptoms being 5 months (range 4-7). Median age was 62 years (range 59-83), all 3 patients were females and functionally independent before symptom onset. Out of 3 patients 2 had HER2+ breast cancer (one with IHC 3+ and one with equivocal IHC but 20 HER2 signals/nucleus) and the third had ovarian carcinoma. All 3 patients had stage IIIA disease as per AJCC 8th edition and presented with bilateral extremity weakness, ataxia, visual disturbances, vertigo and nausea/vomiting. Extensive neurological work up including MRI brain, CSF analysis, EEG were inconclusive except for high titres of anti- Yo antibodies in all patients. All patients were treated with cancer directed therapy and immunomodulation with plasma exchange, IVIG and steroids. The median OS being 22 months (range 12-28) with 2 patients with underlying breast cancer alive at the time of the analysis albeit there has been no neurological recovery, despite IVIG, steroids, and plasma exchange. Conclusions: The anti-Yo associated paraneoplastic ataxic syndrome most commonly associated with breast and pelvic tumors in women has a very poor prognosis despite anti-tumor and immunomodulating therapies, leaving most patients bed-ridden. The neurologic damage is irreparably incurred once the antibodies attack cerebellar cells. Thus, it is critical for clinicians to recognize the potential signs and symptoms as early as possible, so that treatment can be started, and long term symptoms are minimized. Further studies are needed to know the exact mechanism of this syndrome and provide evidence based treatment options.

Cytoplasmic diversity of potato relatives preserved at Plant Breeding and Acclimatization Institute in Poland

Among different types of potato cytoplasmic genomes, some are associated with male sterility or affect agronomic traits. The goal of this study was to analyze types of chloroplast and mitochondrial genomes of selected potato relatives originating from collection of the Institute of Plant Industry, Saint Petersburg, Russia, and preserved in Poland. Using chloroplast and mitochondrial markers the cytoplasm types were determined for 401 genotypes belonging to 43 seed accessions of 28 Solanum species. Among characterized genotypes, 201 (50.1%), 156 (38.9%) and 44 (11%) had cytoplasm types W, D, M, respectively. No accessions with the T, P or A cytoplasm were found. Within cytoplasm W, genotypes with the subtypes: W/α and W/β were identified, but not with W/γ. In S. famatinae, we detected unusual product of the T marker with 65 bp insertion earlier seen exclusively in S. vernei. Among the genotypes of S. leptophyes, two profiles of the ALM_4/ALM_5 marker were observed. S. famatinae and S. vernei come from Argentina, provinces Catamarca and Tucumán. Possibly the insertion in marker T occurred independently in two species, or the accessions were misidentified. Segregation of the ALM_4/ALM_5 marker within S. leptophyes indicates that potato seed accessions are heterogeneous not only due to nuclear DNA polymorphisms but have diversified cytoplasm, too. Our findings are important for exploitation of the tested material in potato breeding. Male-fertile cytoplasm types give a chance of avoiding fertility problems and widening the range of crosses in future generations of breeding materials.