Early detection of dark-affected plant mechanical responses using enhanced electrical signals.

BACKGROUND: Mechanical damage to plants triggers local and systemic electrical signals that are eventually decoded into plant defense responses. These responses are constantly affected by other environmental stimuli in nature, for instance, light fluctuation. In recent years, studies on decoding plant electrical signals powered by various machine learning models are increasing in a sense of early prediction or detection of different environmental stresses that threaten plant growth or crop yields. However, the main bottleneck is the low-throughput nature of plant electrical signals, making it challenging to obtain a substantial amount of training data. Consequently, training these models with small datasets often leads to unsatisfactory performance. RESULTS: In the present work, we set out to decode wound-induced electrical signals (also termed slow wave potentials, SWPs) from plants that are deprived of light to different extents. Using non-invasive electrophysiology, we separately collected sets of local and distal SWPs from the treated plants. Then, we proposed a workflow based on few-shot learning to automatically identify SWPs. This workflow incorporates data preprocessing, feature extraction, data augmentation and classifier training. We established the integral and the first-order derivative as features for efficiently classifying SWPs. We then proposed an Adversarial Autoencoder (AAE) structure to augment the SWP samples. Combining them, the Random Forest classifier allowed remarkable classification accuracies of 0.99 for both local and systemic SWPs. In addition, in comparison to two other reported methods, our proposed AAE structure enabled better classification results using our tested features and classifiers. CONCLUSIONS: The results of this study establish new features for efficiently classifying wound-induced electrical signals, which allow for distinguishing dark-affected local and systemic plant wound responses. We also propose a new data augmentation structure to generate virtual plant electrical signals. The methods proposed in this study could be further applied to build models for crop plants using electrical signals as inputs, and also to process other small-scale signals.

ACA pumps maintain leaf excitability during herbivore onslaught.

Recurrent damage by lepidopteran folivores triggers repeated leaf-to-leaf electrical signaling. We found that the ability to propagate electrical signals-called slow wave potentials-was unexpectedly robust and was maintained in plants that had experienced severe damage. We sought genes that maintain tissue excitability during group insect attack. When Arabidopsis thaliana P-Type II Ca2+-ATPase mutants were mechanically wounded, all mutants tested displayed leaf-to-leaf electrical signals. However, when the auto-inhibited Ca2+-ATPase double-mutant aca10 aca12 was attacked by Spodoptera littoralis caterpillars, electrical signaling failed catastrophically, and the insects consumed these plants rapidly. The attacked double mutant displayed petiole base deformation and chlorosis, which spread acropetally into laminas and led to senescence. A phloem-feeding aphid recapitulated these effects, implicating the vasculature in electrical signaling failure. Consistent with this, ACA10 expressed in phloem companion cells in an aca10 aca12 background rescued electrical signaling and defense during protracted S. littoralis attack. When expressed in xylem contact cells, ACA10 partially rescued these phenotypes. Extending our analyses, we found that prolonged darkness also caused wound-response electrical signaling failure in aca10 aca12 mutants. Our results lead to a model in which the plant vasculature acts as a capacitor that discharges temporarily when leaves are subjected to energy-depleting stresses. Under these conditions, ACA10 and ACA12 function allows the restoration of vein cell membrane potentials. In the absence of these gene functions, vascular cell excitability can no longer be restored efficiently. Additionally, this work demonstrates that non-invasive electrophysiology is a powerful tool for probing early events underlying senescence.

Joint association of complement component 3 and CC-cytokine ligand2 (CCL2) or complement component 3 and CFH polymorphisms in age-related macular degeneration.

BACKGROUND: To determine the joint effect of complement component 3(C3 R102G) with CC-cytokine ligand2 (CCL2-2518) or complement factor H (CFH) Y402H polymorphisms on advanced age-related macular degeneration (AMD). METHODS: In this case-control study, 233 patients with advanced AMD and 159 unrelated healthy controls enrolled for evaluation. Selected polymorphisms were determined by polymerase chain reaction and restriction fragment length polymorphism. RESULTS: A combination of AA CCL2 (rs1024611) and GG C3 (R102G) genotypes resulted in a super-additivity of the risks: OR = 10.13, 95% CI 1.04-98.49, p = 0.04, adjusted OR = 7.74, 95% CI 0.71-84.75, p < 0.1, adjusted synergy indices: relative excess risk due to interaction (RERI) = 1.38, the attributable proportion due to interaction (AP) = 24.7% and the synergy index (S) = 1.43. Combination of at-risk genotypes of CFH Y402H and C3 R102G resulted in a strong super-additive risk: adjusted OR = 22.65, 95% CI 2.32-220.91, p = 0.007, adjusted AP = 90.4% and the S = 12.86. Attributable proportion of risk owing to C3-CCL2 and C3-CFH interaction calculated at 25% and 90% for advanced AMD. CONCLUSION: We have previously shown a strong association of C3 (R102G) and CFH Y402H with AMD whereas no association was found for CCL2-2518. This study enclosed strong synergistic association of risk genotypes of C3 and CFH Y402H with AMD. We also revealed synergistic influence of CCL2-2518 and the at-risk genotype of the C3 in AMD with an estimated AP = 50.9% (adjusted AP = 24.7%). Present findings show that CCL2-2518 polymorphism is not an innocent bystander in AMD susceptibility when combined with the at-risk genotype of C3 (R102G).

Association of polymorphisms in complement component 3 with age-related macular degeneration in an Iranian population.

BACKGROUND: Age related macular degeneration (AMD) is the leading cause of irreversible blindness in the elderly population. Inflammatory mediators play an important role in AMD pathogenesis and immune-related gene polymorphisms are shown to increase the risk. Complement system is an important mediator of the immunity system and several genes encoding proteins involved in this system are associated with susceptibility to AMD. The central element of the complement cascade, C3 has been a plausible candidate since its cleavage product C3a was found in drusen. This study was planned to evaluate the association of C3-rs2230199 (R102G) variants with advanced type AMD in this cohort. MATERIALS AND METHODS: In this case-control study, 494 participants consisting of 266 AMD patients (187 wet AMD and 79 advanced dry AMD) and 228 samples from unrelated healthy controls were enrolled for evaluation. Extracted-DNA samples were amplified to obtain fragments including the polymorphic region. RESULTS: The distribution of the R102G genotypes was significantly different in the AMD patients compared to controls (p = 0.001).The Odds Ratio compared to CC individuals was 1.69 (95% CI 1.15-2.49) for GC individuals and 6.48 (95% CI1.87-22.43) for GG individuals. The Odds Ratio compared to the C allele was 2.31 (95% CI 0.48-11) for the G allele. GG and GC genotypes and G allele were significantly associated with both types of advanced-AMD. Individuals carrying GG genotype have over a six-fold risk of developing AMD in comparison to those carrying the CC genotype in this cohort. Our meta-analysis pooled data showed that our homozygous individuals for GG have a higher risk of AMD compared to previous publications in different nations (p = 0.017). CONCLUSIONS: Our study shows C3 to be a relatively strong susceptibility gene for advanced-type-AMD (exudative-and-geographic-atrophy) in an Iranian population.

Association between proto-oncogene mutations and clinicopathologic characteristics and overall survival in colorectal cancer in East Azerbaijan, Iran.

BACKGROUND: Colorectal cancer (CRC) is the third-most common cancer in Iran. The increasing incidence of CRC in the past three decades has made it a major public health burden in the country. This study aimed to determine any relationship of specific mutations in CRCs with clinicopathologic aspects and outcome of patients. MATERIALS AND METHODS: This study was conducted on 100 CRC patients by the case-only method. Polymerase chain-reaction products were analyzed by Sanger sequencing, and sequence results were compared with the significant KRAS and BRAF gene mutations in the My Cancer Genome database. Logistic regression models were used to detect associations of clinicopathologic characteristics with each of the mutations. Kaplan-Meier and Cox regression models were constructed to estimate overall survival in patients. RESULTS: A total of 26 subjects (26%) had heterozygote-mutant KRAS, and mutations were not detected in the amplified exon of BRAF in both tumor and normal tissues of the 100 CRCs. Rectal tumors had 1.53-fold higher likelihood of KRAS mutations than colon tumors, and men had 1.37-fold higher odds than women. The presence of metastasis increased the likelihood of KRAS mutations 2.36-fold over those with nonmetastatic CRCs. Compared to patients with KRAS wild-type cancers, those with KRAS mutations had significantly higher mortality (hazard ratio 3.74, 95% confidence interval 1.44-9.68; log-rank P=0.003). CONCLUSION: Better understanding of the causality of CRC can be established by combining epidemiology and research on molecular mechanisms of the disease.

Evaluation of CC-cytokine ligand 2 and complementary factor H Y402H polymorphisms and their interactional association with age-related macular degeneration.

PURPOSE: To evaluate the association of CC-cytokine ligand 2 CCL2-2518 (rs1024611) single nucleotide polymorphism, complement factor H (CFH Y402H) and their possible interaction in developing advanced age-related macular degeneration (AMD). METHODS: In this case-control study, DNA samples from 266 patients with advanced AMD and 229 healthy controls were genotyped for CCL2 polymorphism and also 254 patients and 164 healthy controls were genotyped for CFH polymorphism. The possible associations of these polymorphisms with susceptibility to AMD independently and in different joint combinations were evaluated. RESULTS: The genotype frequency for CFH was found to be significantly different between AMD and normal controls (31.5% versus 20.7%, OR = 3.56, p < 0.001 for CC and 52.4% versus 41.5%, OR = 2.96, p < 0.001 for CT genotype). However, no significant association between CCL2 polymorphism and AMD was observed in this cohort (OR = 1.15 and OR = 0.8, p = 0.172). Interestingly, studying the joint effects of two genotypes (TT genotype of CFH Y402H and AG genotype of CCL2-2518) showed more significant protective effect against AMD (p = 0.0001), while the risk effect of CC and CT genotypes of CFH was only visible in the presence of AA genotype of CCL2-2518 (p = 0.044 and p = 0.05). CONCLUSION: Complement factor H Y402H polymorphism is strongly associated with advanced type AMD. Although this study revealed no association of CCL2-2518 with AMD, the risk effect of CFH genotypes was only visible in the presence of AA genotype of CCL2-2518. AG genotype of CCL2-2518 in combination with TT genotype of CFH Y402H showed significant protective effect against AMD.

Tumour necrosis factor-alpha gene polymorphisms in Iranian patients with biliary atresia.

BACKGROUND: Biliary atresia (BA) is a progressive inflammatory destructive process of the bile ducts. This study evaluated the relationship between single-nucleotide polymorphisms in the promoter region of tumour necrosis factor-alpha (TNF-α) gene and bilaiary atresia. MATERIALS AND METHODS: Genomic deoxyribonucleic acid from 16 patients with established diagnosis of BA and 36 patients with INC was obtained. The genotypes of TNF-α-1031 (T/C) and TNF-α-308 (G/A) were determined using the restriction fragment length polymorphism-polymerase chain reaction and the results were analysis with proper statistic software. RESULTS: The frequencies of T/T, T/C in TNF-α-1031 and G/G, G/A in TNF-α-308 were as same as control group. Moreover, we have same deduction for allele frequency and haplotypes analysis (T allele: 84.37%; G allele: 87.5%) in BA patients (T allele: 80.56%; G allele: 86.11%) in controls. In all cases variants of polymorphism did not affect the severity or incidence of BA disease. CONCLUSION: although no significant associations were found between BA and control groups, it seems meaningful that since the nature of BA is multi factorial. Next step will be considering a new target such as downstream modulation of the TNF-α pathway or other cytokines and chemokines which act directly/indirectly.

Spectrum and frequency of GJB2 mutations causing deafness in the northwest of Iran.

OBJECTIVE: Mutations in GJB2 and GJB6 which comprise DFNB1 locus cause up to half of all cases of the prelingual autosomal recessive non-syndromic hearing loss (ARNSHL) worldwide. This study has intended to assess the spectrum and frequency of GJB2/GJB6 mutations in northwest of Iran. METHODS: 508 Patients with presumed ARNSHL were analyzed by applying ARMS-PCR, SSCP, PCR-RFLP and sequencing assays. RESULTS: Seventy-five (14.7%) different homozygous and eighty-seven (17.1%) different compound heterozygous genotypes were detected in this cohort. Concerning the GJB2 gene, c.35delG was the most prevalent mutation, accounting for 16.4% of the samples. In addition 29 sequence variations other than c.35delG mutation were distinguished in GJB2; namely, delE120, Ins A 290-291, R143Q, V37I, R32H, Y155X, V27I + T123N, F154F, 167delT, 312del14, 299-300delA, T8M, W24X, E114G + V27I, 235delC, R184P, V153I, S139N, A171T, M163V (unknown mutation), G127V, E147X, R127H, 35insG, R143W, V27I, G160S, E114G and IVS1 + 1G > A. Moreover, the IVS1 + 1G > A was accounted as a second common mutation. CONCLUSIONS: Overall, the frequency of GJB2 mutations (≥31%) is in agreement with other white population. These findings highlight the importance of the study of GJB2 gene in the diagnosis to provide early treatment and genetic counseling.

R229Q polymorphism of NPHS2 gene in patients with late-onset steroid-resistance nephrotic syndrome: a preliminary study.

INTRODUCTION: Depending on the response to standard steroid therapy, nephrotic syndrome it is classified to steroid-sensitive and steroid-resistant nephrotic syndrome (SRNS). Mutations in several genes including NPHS2 have been implicated in SRNS. Gene R229Q polymorphism (p.R229Q) of NPHS2 is associated with adolescent- or adult-onset SRNS in European and South American populations. We investigated this polymorphism among a group of Iranian-Azeri patients with primary SRNS. MATERIALS AND METHODS: All participants had the primary late-onset form of focal segmental glomerulosclerosis (FSGS) and their clinical feature was steroid unresponsiveness. They were compared with a group of age- and sex-matched individuals without any renal disease for NPHS2 gene as controls. The R229Q polymorphism (p.R229Q) was investigated in the case and control groups. RESULTS: A total of 25 patients (mean age, 26.6 +/- 8.0 years) with primary FSGS and 35 controls (mean age, 26.0 +/- 8.7 years) were studied. Serum creatinine of patients and their 24-hour protein excretion at the time of study were 2.4 +/- 1.94 mg/dL and 2830 +/- 981 mg/dL, respectively. Molecular study showed no p.R229Q polymorphism, neither in patients nor in controls. CONCLUSIONS: In this preliminary study, we showed that NPHS2 gene p.R229Q polymorphism does not present in Iranian-Azeri population with SRNS. Larger studies are needed to confirm our results and other mutated genes should also be considered in these patients.

Whole-exome sequencing efficiently detects rare mutations in autosomal recessive nonsyndromic hearing loss.

Identification of the pathogenic mutations underlying autosomal recessive nonsyndromic hearing loss (ARNSHL) is difficult, since causative mutations in 39 different genes have so far been reported. After excluding mutations in the most common ARNSHL gene, GJB2, via Sanger sequencing, we performed whole-exome sequencing (WES) in 30 individuals from 20 unrelated multiplex consanguineous families with ARNSHL. Agilent SureSelect Human All Exon 50 Mb kits and an Illumina Hiseq2000 instrument were used. An average of 93%, 84% and 73% of bases were covered to 1X, 10X and 20X within the ARNSHL-related coding RefSeq exons, respectively. Uncovered regions with WES included those that are not targeted by the exome capture kit and regions with high GC content. Twelve homozygous mutations in known deafness genes, of which eight are novel, were identified in 12 families: MYO15A-p.Q1425X, -p.S1481P, -p.A1551D; LOXHD1-p.R1494X, -p.E955X; GIPC3-p.H170N; ILDR1-p.Q274X; MYO7A-p.G2163S; TECTA-p.Y1737C; TMC1-p.S530X; TMPRSS3-p.F13Lfs*10; TRIOBP-p.R785Sfs*50. Each mutation was within a homozygous run documented via WES. Sanger sequencing confirmed co-segregation of the mutation with deafness in each family. Four rare heterozygous variants, predicted to be pathogenic, in known deafness genes were detected in 12 families where homozygous causative variants were already identified. Six heterozygous variants that had similar characteristics to those abovementioned variants were present in 15 ethnically-matched individuals with normal hearing. Our results show that rare causative mutations in known ARNSHL genes can be reliably identified via WES. The excess of heterozygous variants should be considered during search for causative mutations in ARNSHL genes, especially in small-sized families.

Prevalence of IVS1+1G>A mutation among Iranian Azeri Turkish patients with autosomal recessive non-syndromic hearing loss (ARNSHL).

OBJECTIVE: Mutations in the GJB2 gene has been reported as a main cause for autosomal recessive non-syndromic hearing loss (ARNSHL) all over the world. IVS1+1G>A which is splice site mutation have been detected in several populations as disruptive mutation. This study has intended to assess the significance of this mutation, IVS1+1G>A, to the autosomal recessive non-syndromic genetic load among Iranian Azeri Turkish patients. METHODS: Following our previous study, one hundred and seventy four unrelated patients with prelingual ARNSL were included in this study. Thirty nine patients had only one identified mutated allele, whereas hundred and thirty five patients were negative for coding region of GJB2. All these patients were screened for IVS1+1G>A by applying PCR-RFLP assay. RESULTS: Among studied patients nine compound heterozygote with 35delG, delE120, 235delC were identified. Additionally, six patients were detected with only one IVS1+1G>A mutated allele. In these patients, the other mutated allele was left unidentified. One patient was identified to be homozygous for IVS1+1G>A. Further studies carried out on parents of positive cases, showed that one of the healthy parents (mother) to be homozygous for IVS1+1G>A mutation. By self-report, this person had no hearing impairment, although it is possible that she has mild or moderate hearing loss, which she is unable to detect. Her child was compound heterozygous (IVS1+1G>A/35delG) with profound deafness. The frequency of IVS1+1G>A was found to be about 4.9%, however the parental consanguinity was observed in 37.5% of IVS1+1G>A-mutated families. CONCLUSIONS: Our results support founder effect regarding these mutations and the presence of an ancient ancestor is strengthened in comparison to hot spot hypothesis. Also the results suggest variable expressivity of IVS1+1G>A mutation with respect to hearing loss.