Complete Homology Research Articles

Identification of a New B-Cell Epitope on the Capsid Protein of Avian Leukosis Virus and Its Application.

Avian leukosis virus (ALV) is an avian oncogenic retrovirus that can impair immunological function, stunt growth and decrease egg production in avian flocks. The capsid protein (P27) is an attractive candidate for ALV diagnostics. In the present study, a new hybridoma cell (1F8) stably secreting an anti-P27 monoclonal antibody (mAb) was developed. The mAb exhibited a high affinity constant (Ka) of 8.65 × 106.0 L/mol, and it could be used for the detection of ALV-A/B/J/K strains. Moreover, a total of eight truncated recombinant proteins and five synthetic polypeptides were utilized for the identification of the B-cell epitopes present on P27. The results revealed that 218IIKYVLDRQK227 was the minimal epitope recognized by 1F8, which had never been reported before. Additionally, the epitopes could strongly react with different ALV subgroup's specific positive serum and had a complete homology among all the ALV subgroups strains. Finally, a new sandwich ELISA method was created for the detection of ALV antigens, demonstrating increased sensitivity compared to a commercially available ELISA kit. These results offer essential knowledge for further characterizing the antigenic composition of ALV P27 and will facilitate the development of diagnostic reagents for ALV.

Complete Loss ofRelA andSpoT Homologs inArabidopsis Reveals the Importance ofthe Plastidial Stringent Response inthe Interplay between Chloroplast Metabolism andPlant Defense Response.

The highly phosphorylated nucleotide, guanosine tetraphosphate (ppGpp), functions as a secondary messenger in bacteria and chloroplasts. The accumulation of ppGpp alters plastidial gene expression and metabolism, which are required for proper photosynthetic regulation and robust plant growth. However, because four plastid-localized ppGpp synthases/hydrolases function redundantly, the impact of the loss of ppGpp-dependent stringent response on plant physiology remains unclear. We used CRISPR/Cas9 technology to generate an Arabidopsis thaliana mutant lacking all four ppGpp synthases/hydrolases and characterized its phenotype. The mutant showed over 20-fold less ppGpp levels than the wild type under normal growth conditions and exhibited leaf chlorosis and increased expression of defense-related genes as well as salicylic acid and jasmonate levels upon transition to nitrogen-starvation conditions. These results demonstrate that proper levels of ppGpp in plastids are required for controlling not only plastid metabolism but also phytohormone signaling, which is essential for plant defense.

Epidemiology and molecular characterization of Feline panleukopenia virus from suspected domestic cats in selected Bangladesh regions.

Feline panleukopenia (FPL) is a highly contagious cat disease and is endemic in Bangladesh. The study aims to describe the epidemiology and molecular characterization of the Feline panleukopenia virus from the suspected domestic cats in selected Bangladesh regions. Randomly, 161 rectal swabs were collected from the pet hospitals between July 2021 and December 2022. A structured questionnaire was administered through face-to-face interviews with cat owners in order to collect data on potential risk factors for FPL, such as age, sex, sharing litter boxes and every day utensils in multicat households, vaccination history, hospital visits for other diseases, and season. The rectal swabs were tested by PCR targeting the VP2 capsid protein gene, and six PCR-positive samples were further sequenced for molecular characterizations. The risk factors for FPLV were identified using multivariable logistic regression analysis. The overall prevalence of FPL among suspects was 22.9%. The mortality and case fatality were 10.6%, and 45.9%, respectively. However, mortality in kittens was significantly higher (16.4%) than younger cats. The odds of FPL were 8.83 times (95% CI: 3.14-24.85) higher among unvaccinated cats than vaccinated cats. The winter season had almost six times (95% CI: 1.38-24.40) higher odds of FPL than rainy season. In a multicat house, the odds of FPL was about five times (95% CI: 1.93-13.45) higher for cats that shared a litter box and food utensils compared to those that did not engage in such sharing. Visiting hospitals for other reasons nearly triples the odds of FPL (OR: 2.80, 95% CI: 1.04-7.54) compared to cats that do not visit hospitals. Analysis of partial sequence of the VP2 gene revealed genetic variations among the isolates from different regions. Among these isolates, four were identical to FPLV isolates from South Korea and China, while one showed complete homology with FPLV isolates from Thailand. In contrast, the remaining one was 100% identical to Carnivore protoparvovirus-1 isolated from a feline sample in Italy. Our isolates were classified into three distinct clades alongside Feline panleukopenia virus and Carnivore protoparvovirus-1. One in every three suspected cats was infected with Feline panleukopenia. Regular vaccination of the cats, especially those that share common litter box and food utensils and visit hospitals for other purposes, will help reduce the prevalence of FPL in Bangladesh. Besides, it is worth emphasizing the existence of genetic diversity among the circulating Feline panleukopenia viruses in Bangladesh.

On the étale cohomology of Hilbert modular varieties with torsion coefficients

We study the étale cohomology of Hilbert modular varieties, building on the methods introduced by Caraiani and Scholze for unitary Shimura varieties. We obtain the analogous vanishing theorem: in the ‘generic’ case, the cohomology with torsion coefficients is concentrated in the middle degree. We also probe the structure of the cohomology beyond the generic case, obtaining bounds on the range of degrees where cohomology with torsion coefficients can be non-zero. The proof is based on the geometric Jacquet–Langlands functoriality established by Tian and Xiao and avoids trace formula computations for the cohomology of Igusa varieties. As an application, we show that, when $p$ splits completely in the totally real field and under certain technical assumptions, the $p$-adic local Langlands correspondence for $\mathrm {GL}_2(\mathbb {Q}_p)$ occurs in the completed homology of Hilbert modular varieties.

Expression of recombinant Omp18 and MOMP of Campylobacter jejuni and the determination of their suitability as antigens for serological diagnosis of campylobacteriosis in animals.

Campylobacteriosis causes gastrointestinal tract lesions in adults and children and may result in severe complications. The primary sources of infection are infected animals and animal products. Immunochemical methods effectively diagnose intestinal infections but require highly specific antigens to detect their antibodies. This study aimed to obtain two recombinant immunogenic antigens of Campylobacter jejuni, an outer membrane protein with a molecular weight of 18 kDa (Omp18) and the major outer membrane protein (MOMP) with a molecular weight of 45 kDa, and evaluate their suitability for the serological diagnosis of campylobacteriosis using immunochromatographic assay (ICA). The C. jejuni Omp18 and MOMP gene sequences were synthesized de novo (Macrogen, Korea) and cloned into the pET32 expression plasmid. Using these genetic constructs, electrocompetent cells of the Escherichia coli BL21 strain were transformed and cultured under various conditions. Antigens were purified and refolded using metal affinity chromatography. The properties of the purified proteins were studied by western blotting, liquid chromatography with tandem mass spectrometry, and enzyme-linked immunosorbent assay (ELISA). We developed two recombinant E. coli BL21 cells producing rOmp18 and Recombinant MOMP (rMOMP) antigens with molecular weights of 36 and 64 kDa, respectively. Amino acid sequence analysis of the obtained antigens showed complete homology with the reference sequences in the PubMed NCBI database. Western blotting using positive-control sera demonstrated the specificity of the recombinant antigens. The results of ELISA with 94 bovine sera showed the interaction of recombinant antigens with specific antibodies. The obtained rOmp18 and rMOMP antigens can detect antibodies in the serum of infected or recovered animals and can be used to develop ICA.

The S protein of a novel recombinant PEDV strain promotes the infectivity and pathogenicity of PEDV in mid-west China.

Porcine epidemic diarrhoea virus (PEDV) is an emerging and re-emerging swine enterovirus that causes highly contagious diarrhoea and mortality in piglets. To better understand the current prevalence of PEDV in mid-west China, and to find out the reason for the re-emergence of PEDV from the viral genomic characteristics. Herein, we firstly investigated epidemiology of PEDV in mid-west China from 2019 to 2020. A total of 62.23% (257/413) of diarrhoea samples were positive for PEDV, and the PEDV-positive cases were mainly detected in winter. Then, we selected the SXSL strain as a representative strain to study the genetic and pathogenic characterization of PEDV pandemic strains in mid-west China. The recombination analysis showed that SXSL strain was a recombinant strain, and the major and minor parent strains of the recombination are CH/SCZJ/2018 strain and GDS48 strain, respectively. Complete genome sequencing and homology analysis showed that the S protein of SXSL strain contained multiple amino acid indels and mutations compared to the PEDV representative strains. Furthermore, we evaluated the effect of S protein on the infectivity and pathogenicity of PEDV by the PEDV reverse genetics system, and results showed that SXSL S protein increased the infectivity and pathogenicity of chimeric virus. Overall, our findings provided important information for understanding the roles of S protein in the prevalence of PEDV in mid-west China and developing vaccines based on PEDV pandemic strains.

Genetic Signature and Serocompatibility Evidence for Drug Resistant Campylobacter jejuni.

Campylobacteriosis, a foodborne illness, is one of the world′s leading causes of gastrointestinal illness. This study investigates the link between human campylobacteriosis and the consumption of potentially contaminated food with Campylobacter jejuni. Three hundred sixty samples were collected from humans, chicken cloaca, raw chicken meat, unpasteurized milk, and vegetables. The chickens were obtained from licensed and non-licensed slaughterhouses, and only the necks and wings were studied. Samples were enriched under microaerobic conditions then cultured on the modified charcoal cefoperazone deoxycholate agar. Bacteria was identified by staining, biochemical testing, and molecular identification by the polymerase chain reaction for the virulence genes; hipO, asp, dnaJ, cadF, cdtA, cdtB, and cdtC. The genomic homogeneity of C. jejuni between human and chicken isolates was assessed by the serological Penner test and the pulse field gel electrophoresis (PFGE). Campylobacter was not detected in the vegetables and pasteurized milk, though, only twenty isolates from chickens and clinical samples were presumed to be Campylobacter based on their morphology. The biochemical tests confirmed that five isolates were C. coli, and fifteen isolates were C. jejuni including two isolates from humans, and the remaining were from chickens. The colonization of C. jejuni in chickens was significantly lower in necks (6.66%) obtained from licensed slaughterhouses compared to those obtained from non-licensed slaughterhouses (33.3%). The antimicrobial susceptibility test showed that all identified C. jejuni isolates were resistant to antibiotics, and the majority of isolates (53.5%) showed resistance against six antibiotics, though, all isolates were resistant to ciprofloxacin, tetracycline, and aztreonam. The Penner test showed P:21 as the dominant serotype in isolates from humans, necks, and cloaca. The serohomology of C. jejuni from human isolates and chicken necks, wings, and cloaca was 71%, 36%, 78%, respectively. The PFGE analysis of the pattern for DNA fragmentation by the restriction enzyme Smal showed a complete genotypic homology of C. jejuni human isolates and chicken necks compared to partial homology with cloacal isolates. The study brings attention to the need for effective interventions to ensure best practices for safe poultry production for commercial food chain supply to limit infection with foodborne pathogens, including Campylobacter.

Isolation and characterization of Mycoplasma hominis from the semen of infertile men and detection of virulence factors genes

The bacterial infection of seminal fluid is one of the most important factors behind infertility in many cases. The biological diversity of the Mycoplasma have widely been reported to be associated with the infertility grade in many cases. This study was conducted to identify and characterize the identity and the phylogenetic positioning of Fourteen isolates of Mycoplasma in seminal fluids. three genetic loci were included in this study 16S rRNA, recA, and Vaa for Mycoplasma sequences. Each amplified locus was investigated in both bacterial infections to identify the identity of the possible bacterial infection of those patients and to assess the pattern of the genetic variation for each genetic locus in the investigated patients. Our results indicated a complete homology with the referring sequences of Mycoplasma hominis (GenBank acc. no. CP055150.1). Concerning the 16S rRNA fragment, no genetic variation was found in the investigated samples. It was inferred from the tree that the investigated samples were suited in the immediate vicinity to many strains of Mycoplasma hominis belonging to various European origins. Furthermore, the patterns of the neighbour phylogenetic distances in this tree indicated a specific biological diversity of the incorporated Mycoplasma hominis sequences.

Homology Modeling of Predicted Methyl Transferases (STY 3264): A Protein of Salmonella TYPHI CT18

Background: Salmonella typhi gives rise to typhoid fever which is life threatening illness.It puts end to approximately 600,000 people per annum around the world.Food and water are the leading components through which this disease is passed on and becomes origin of typhoid.It lays out widely where cleanliness is very substandard. Objective: To construct 3 dimensional structure of protein Methyl Transferase of Salmonella typhi CT18 by homology modeling. Materials and Methods: Bioinformatic tools and programs like Comprehensive Microbial Resource (CMR), Interproscan, Basic Local Alignment Search Tool (BLAST), Modellor 9.10, Procheck and Prosa were helpful for the complete homology modeling of methyl transferases (STY 3264).The models were visualized by DS Viever. Results: Homology modeling is an effective method to find structure of methyl transferase protein for future discovery of drugs. Conclusion: Homology modeling is an effective method to find structure of protein which provides good solution for drug discovery. Keywords: Methyl transferase ,Homology modeling, Typhoid fever,Salmonella typhi CT18.

​Prevalence Risk Factor Analysis and Molecular Characterization of Canine Monocytic Ehrlichiosis in Maharashtra

Background: The research work was undertaken with the aim to investigate the prevalence and influence of associated risk factors on canine monocytic ehrlichiosis (CME), by employing conventional and molecular techniques in naturally occurring ehrlichiosis in dogs from the geographical area of Pune and Satara, Maharashtra, India. Methods: Evaluation of 60 blood samples from dogs exhibiting illness clinically suggestive of CME was performed for the detection of Ehrlichia canis by conventional microscopy and PCR-based assays targeting 16S rRNA gene. The collected blood samples were also utilized immediately for estimation of haemato-biochemical parameters. Descriptive statistics along with chi-square test of association were performed by using SPSS software. Result: Microscopic examination of Geimsa stained thin blood smears revealed Ehrlichia canis morulae in 5.00% (03/60) samples. Processing of purified DNA from blood samples by Genus-specific 16SrRNA PCR, with known primers resulted in amplification of 477 bp product of 6.66% (04/60) samples evident of CME. Further two step nested PCR assay using published species-specific primers yielded 387 bp product in 16.66% (10/60) samples indicative of E. canis. Younger, exotic cross breed females dogs were found more prone compared to adults. Indian non-descript male counterparts and winter season being more favorable for CME. Sequence analysis of randomly selected representative samples from Pune and Satara each when aligned with nine isolates from India and western countries showed complete homology.

Vanishing theorems for Shimura varieties at unipotent level

We show that the compactly supported cohomology of Shimura varieties of Hodge type of infinite \Gamma_1(p^\infty) -level (defined with respect to a Borel subgroup) vanishes above the middle degree, under the assumption that the group of the Shimura datum splits at p . This generalizes and strengthens the vanishing result proved in [A. Caraiani et al., Compos. Math. 156 (2020)]. As an application of this vanishing theorem, we prove a result on the codimensions of ordinary completed homology for the same groups, analogous to conjectures of Calegari–Emerton for completed (Borel–Moore) homology.

The Fontaine-Mazur conjecture in the residually reducible case

We prove new cases of Fontaine-Mazur conjecture on two-dimensional Galois representations overQ\mathbb {Q}when the residual representation is reducible. Our approach is via a semi-simple local-global compatibility of the completed cohomology and a Taylor-Wiles patching argument for the completed homology in this case. As a key input, we generalize the work of Skinner-Wiles in the ordinary case. In addition, we also treat the residually irreducible case at the end of the paper. Combining with people’s earlier work, we can prove the Fontaine-Mazur conjecture completely in the regular case whenp≥5p\geq 5.

Corrigendum to Complete homology and related dimensions of groups [J. Group Theory 12 (2009), 431–448

Article Corrigendum to Complete homology and related dimensions of groups [J. Group Theory 12 (2009), 431–448] was published on November 1, 2021 in the journal Journal of Group Theory (volume 24, issue 6).

Exploring the Origin and Relatedness of Maternal Lineages Through Analysis of Mitochondrial DNA in the Holstein Horse.

Maternal lineages are important for the breeding decision in the Holstein horse breed. To investigate the genetic diversity of the maternal lineages and the relationships between founder mares, the maternal inherited mitochondrial genome (except the repetitive part of the non-coding region) of 271 mares representing 75 lineages was sequenced. The sequencing predominantly revealed complete homology in the nucleotide sequences between mares from one lineage with exceptions in 13 lineages, where differences in one to three positions are probably caused by de novo mutations or alternate fixation of heteroplasmy. We found 78 distinct haplotypes that have not yet been described in other breeds. Six of these occurred in two or three different lineages indicating a common ancestry. Haplotypes can be divided into eight clusters with all mares from one lineage belonging to the same cluster. Within a cluster, the average number of pairwise differences ranged from zero to 16.49 suggesting close maternal relationships between these mares. The results showed that the current breeding population originated from at least eight ancestral founder mares.

Risk factors and Molecular genotyping of Brucella melitensis strains recovered from humans and their owned cattle in Upper Egypt

Brucellosis is a zoonosis that has a devastating impact on the economy and public health, particularly in the Middle East, including Egypt. This study aimed to define risk factors associated with brucellosis in humans and in their cattle in Fayoum governorate - Upper Egypt. Also, molecular genotyping of recovered Brucella isolates from human cases and their cattle to assess the potential cross-species transmission in the study region. Data were obtained via double matched case–control studies for brucellosis in humans (106 cases and 160 controls) and in their cattle (78 cattle cases and 105 cattle controls). The results of multivariate regression analysis revealed that predictors of human brucellosis were animal-related occupations (OR 2.1, P 0.02), previous infection in other household members (OR 3.2, P 0.007), eating home-made soft cheese (OR 2.3, P 0.03), and exposure to cattle abortions (OR 6.9, P < 0.001). For cattle, predictors of brucellosis were maturity ≥2 years of age (OR 2.9, P 0.01), ≥2 animals reared by the same household (OR 3.7–6.9, P ≤ 0.001), and recent abortion (OR 15.2, P 0.01). Twelve Brucella isolates were recovered from eight human cases (7.5%, 8/106) and four cattle cases (6.2%, 4/65). All isolates were B. melitensis biovar 3. Analysis of the IS711 gene sequence revealed complete homology (100%) between isolates. Six virulence genes were utilized for virutyping: virB (100%), omp25 (100%), amiC (100%), ure (91.7%), wbkA (91.7%), and bvfA (75%). Virutyping revealed four virutypes: V1 (lack bvfA, 16.7%), V2 (harbored all genes, 66.7%), V3 (lack wbkA, 8.3%), and V4 (lack wbkA and ure, 8.3%). Repetitive extragenic palindromic PCR (REP-PCR) typing revealed two REP types. Combined REP-PCR/virulence genotyping revealed five different genotypes (G1–G5) for the detected isolates and a unique genotype for the reference strain (G6, B. melitensis bv3 Ether). Human and cattle isolates from the same household had matched genotypes. In conclusion, there were widespread risk factors among the cases studied. Health education for high-risk groups is essential for disease prevention, and combined REP-PCR/virulence genotyping is a quick tool for traceability, particularly in developing countries endemic with brucellosis as Egypt.

The C. elegans pseudogene sspt-16 (F55A3.7) is required to safeguard germ cells against reprogramming.

We recently identified FAcilitates Chromatin Transcription (FACT) as a reprogramming barrier of transcription factor (TF) mediated conversion of germ cells into neurons in C. elegans. FACT is a conserved heterodimer consisting of SPT16 and SSRP1 in mammals. Duplication events during evolution in C. elegans generated two SSRP1 homologs named HMG-3 and HMG-4, while SPT-16 is the only homolog of SPT16. Yet, the pseudogene F55A3.7 has nearly complete nucleotide sequence homology to the spt-16 gene. However, F55A3.7 lacks some spt-16 exons and DNA pieces so we named it sspt-16 (short spt-16). Surprisingly, the deletion mutant ok1829, which affects only the sspt-16 pseudogene, shows similar germ cell reprogramming effects as described previously for FACT-depleted animals. We examined whether lack of sspt-16 affects other genes or chromatin accessibility, which may explain the permissiveness for germ cell reprogramming.

Potential Mimicry of Viral and Pancreatic β Cell Antigens Through Non-Spliced and cis-Spliced Zwitter Epitope Candidates in Type 1 Diabetes.

Increasing evidence suggests that post-translational peptide splicing can play a role in the immune response under pathological conditions. This seems to be particularly relevant in Type 1 Diabetes (T1D) since post-translationally spliced epitopes derived from T1D-associated antigens have been identified among those peptides bound to Human Leucocyte Antigen (HLA) class I and II complexes. Their immunogenicity has been confirmed through CD4+ and CD8+ T cell-mediated responses in T1D patients. Spliced peptides theoretically have a large sequence variability. This might increase the frequency of viral-human zwitter peptides, i.e. peptides that share a complete sequence homology irrespective of whether they originate from human or viral antigens, thereby impinging upon the discrimination between self and non-self antigens by T cells. This might increase the risk of autoimmune responses triggered by viral infections. Since enteroviruses and other viral infections have historically been associated with T1D, we investigated whether cis-spliced peptides derived from selected viruses might be able to trigger CD8+ T cell-mediated autoimmunity. We computed in silico viral-human non-spliced and cis-spliced zwitter epitope candidates, and prioritized peptide candidates based on: (i) their binding affinity to HLA class I complexes, (ii) human pancreatic β cell and medullary thymic epithelial cell (mTEC) antigens’ mRNA expression, (iii) antigen association with T1D, and (iv) potential hotspot regions in those antigens. Neglecting potential T cell receptor (TCR) degeneracy, no viral-human zwitter non-spliced peptide was found to be an optimal candidate to trigger a virus-induced CD8+ T cell response against human pancreatic β cells. Conversely, we identified some zwitter peptide candidates, which may be produced by proteasome-catalyzed peptide splicing, and might increase the likelihood of pancreatic β cells recognition by virus-specific CD8+ T cell clones, therefore promoting β cell destruction in the context of viral infections.

Molecular characteristic of treatment failure clinical isolates of Leishmania major.

BackgroundLeishmaniasis is a prevalent tropical disease caused by more than 20 Leishmania species (Protozoa, Kinetoplastida and Trypanosomatidae). Among different clinical forms of the disease, cutaneous leishmaniasis is the most common form, with an annual 0.6–1 million new cases reported worldwide. This disease’s standard treatment is pentavalent antimonial (SbV) that have been used successfully since the first half of the 20th century as a first-line drug. However, treatment failure is an increasing problem that is persistently reported from endemic areas. It is important to define and standardize tests for drug resistance in cutaneous leishmaniasis. SbV must be reduced to its trivalent active form (SbIII). This reduction occurs within the host macrophage, and the resultant SbIIIenters amastigotes via the aquaglyceroporin1 (AQP1) membrane carrier. Overexpression of AQP1 results in hypersensitivity of the parasites to SbIII, but resistant phenotypes accompany reduced expression, inactivation mutations, or deletion of AQP1. Hence, in this study, a phylogenetic analysis using barcode gene COXII and kDNA minicircle and expression analysis of AQP1 were performed in treatment failure isolates to assess the isolates’ molecular characteristics and to verify possible association with drug response.MethodsSamples in this study were collected from patients with cutaneous leishmaniasis referred to the Diagnosis Laboratory Center in Isfahan Province, Iran, from October 2017 to December 2019. Among them, five isolates (code numbers 1–5) were categorized as treatment failures. The PCR amplification of barcode gene COXII and kDNA minicircle were done and subsequently analyzed using MEGA (10.0.5) to perform phylogenetics analysis of Treatment failures (TF) and Treatment response (TR) samples. Relative quantification of the AQP1 gene expression of TF and TR samples was assessed by real-time PCR.ResultsAll samples were classified as L. major. No amplification failure was observed in the cases of barcode gene COXII and kDNA minicircle amplification. Having excluded the sequences with complete homology using maximum parsimony with the Bootstrap 500 method, four major groups were detected to perform phylogenetic analysis using COXII. The phylogenetic analysis using the barcode target of minicircle showed that all five treatment failure isolates were grouped in a separate sub-clade.ConclusionsWe concluded that the barcode gene COXII and the minicircle kDNA were suitable for identification, differentiation and phylogenetic analysis in treatment failure clinical isolates of Leishmania major. Also, AQP1 gene expression analyses showed that treatment failure isolates had less expression than TR isolates. The isolate with TF and overexpression of the AQP1 gene of other molecular mechanisms such as overexpression of ATP-binding cassette may be involved in the TR, such as overexpression of ATP-binding cassette which requires further research.

Incidence coefficients in the Novikov Complex for Morse forms: rationality and exponential growth properties

Let f : M → S 1 be a Morse map, v a transverse f -gradient. Theconstruction of the Novikov complex associates to these data a free chain complexC ∗ (f, v) over the ring Z[t]][t −1 ], generated by the critical points of f and computingthe completed homology module of the corresponding infinite cyclic covering of M .Novikov’s Exponential Growth Conjecture says that the boundary operators in thiscomplex are power series of non-zero convergence raduis.In [12] the author announced the proof of the Novikov conjecture for the case ofC 0 -generic gradients together with several generalizations. The proofs of the firstpart of this work were published in [13]. The present article contains the proofs ofthe second part.There is a refined version of the Novikov complex, defined over a suitable com-pletion of the group ring of the fundamental group. We prove that for a C 0 -genericf -gradient the corresponding incidence coefficients belong to the image in the Novikovring of a (non commutative) localization of the fundamental group ring.The Novikov construction generalizes also to the case of Morse 1-forms. In thiscase the corresponding incidence coefiicients belong to a certain completion of thering of integral Laurent polynomials of several variables. We prove that for a givenMorse form ω and a C 0 -generic ω-gradient these incidence coefficients are rationalfunctions.The incidence coefficients in the Novikov complex are obtained by counting thealgebraic number of the trajectories of the gradient, joining the zeros of the Morseform. There is V.I.Arnold’s version of the exponential growth conjecture, whichconcerns the total number of trajectories. We confirm this stronger form of theconjecture for any given Morse form and a C 0 -dense set of its gradients.We give an example of explicit computation of the Novikov complex.

Multi-tissue transcriptome analysis using hybrid-sequencing reveals potential genes and biological pathways associated with azadirachtin A biosynthesis in neem (azadirachta indica)

BackgroundAzadirachtin A is a triterpenoid from neem tree exhibiting excellent activities against over 600 insect species in agriculture. The production of azadirachtin A depends on extraction from neem tissues, which is not an eco-friendly and sustainable process. The low yield and discontinuous supply of azadirachtin A impedes further applications. The biosynthetic pathway of azadirachtin A is still unknown and is the focus of our study.ResultsWe attempted to explore azadirachtin A biosynthetic pathway and identified the key genes involved by analyzing transcriptome data from five neem tissues through the hybrid-sequencing (Illumina HiSeq and Pacific Biosciences Single Molecule Real-Time (SMRT)) approach. Candidates were first screened by comparing the expression levels between the five tissues. After phylogenetic analysis, domain prediction, and molecular docking studies, 22 candidates encoding 2,3-oxidosqualene cyclase (OSC), alcohol dehydrogenase, cytochrome P450 (CYP450), acyltransferase, and esterase were proposed to be potential genes involved in azadirachtin A biosynthesis. Among them, two unigenes encoding homologs of MaOSC1 and MaCYP71CD2 were identified. A unigene encoding the complete homolog of MaCYP71BQ5 was reported. Accuracy of the assembly was verified by quantitative real-time PCR (qRT-PCR) and full-length PCR cloning.ConclusionsBy integrating and analyzing transcriptome data from hybrid-seq technology, 22 differentially expressed genes (DEGs) were finally selected as candidates involved in azadirachtin A pathway. The obtained reliable and accurate sequencing data provided important novel information for understanding neem genome. Our data shed new light on understanding the biosynthesis of other triterpenoids in neem trees and provides a reference for exploring other valuable natural product biosynthesis in plants.