Review of the current TB human infection studies for use in accelerating TB vaccine development: A meeting report.

Tools to evaluate and accelerate tuberculosis (TB) vaccine development are needed to advance global TB control strategies. Validated human infection studies for TB have the potential to facilitate breakthroughs in understanding disease pathogenesis, identify correlates of protection, develop diagnostic tools, and accelerate and de-risk vaccine and drug development. However, key challenges remain for realizing the clinical utility of these models, which require further discussion and alignment amongst key stakeholders. In March 2023, the Wellcome Trust and the International AIDS Vaccine Initiative (IAVI) convened international experts involved in developing both TB and Bacillus Calmette-Guerin (BCG) human infection studies (including mucosal and intradermal challenge routes) to discuss the status of each of the models and the key enablers to move the field forward. This report provides a summary of the presentations and discussion from the meeting. Discussions identified key issues, including demonstrating model validity, to provide confidence for vaccine developers, which may be addressed through demonstration of known vaccine effects, e.g. BCG vaccination in specific populations, and by comparing results from field efficacy and human infection studies. The workshop underscored the importance of establishing safe and acceptable studies in high-burden settings, and the need to validate more than one model to allow for different scientific questions to be addressed as well as to provide confidence to vaccine developers and regulators around use of human infection study data in vaccine development and licensure pathways.

Fruit Quality Assessment of Novel Hybrid Pummelo × Sweet Orange and Its Molecular Characterization Using Acidity Specific Markers.

Research background: There is considerable diversity in newly developed pummelo × sweet orange citrus hybrids. Most hybrids showed lower peel thickness and high juice yield but there is a lack of information on fruit quality parameters and molecular characterization. Therefore, the aim of the current study is to determine the content of antioxidants and properties of the fresh juice of 24 new pummelo × sweet orange citrus hybrids (Citrus maxima [Burm. f.] Osbeck × Citrus sinensis [L.] Osbeck) and the parental genotypes along with molecular characteristics determined using acidity specific markers. Experimental approach: The correlation and estimate of inheritance of the fruit juice properties: ascorbic acid, total phenol, total flavonoid, total antioxidant, total soluble solid and sugar contents, pH, titratable acidity, along with sensory evaluation was performed. Molecular characterization of these hybrids was carried out using de novo generated acidity specific simple sequence repeat (SSR) markers. Results and conclusions: The main constituents of the fruit juice of pummelo × sweet orange hybrids were observed in the range of w(ascorbic acid)=40.00-58.13 mg/100 g, total phenols expressed as gallic acid equivalents w(GAE)=40.67-107.33 mg/100 g, total antioxidants expressed as Trolox equivalents b(Trolox)=2.03-5.49 µmol/g, total flavonoids expressed as quercetin equivalents w(QE)=23.67-59.33 mg/100 g, along with other properties: total soluble solids=7.33-11.33 %, w(total sugar)=2.10-5.76 %, w(reducing sugar)=1.69-2.78 %, w(non-reducing sugar)=0.39-3.17 % and titratable acidity 1.00-2.11 %. The above parameters differed significantly in the fruit juice of the evaluated pummelo × sweet orange hybrids. Considering these parameters, the hybrids SCSH 17-9, SCSH 13-13, SCSH 11-15 and SCSH 3-15 had superior antioxidant properties in terms of these parameters. A higher heritability (≥80 %) was also observed for all juice properties. Molecular characterization of pummelo × sweet orange hybrids showed that >50 % of the hybrids were grouped with medium acidity parents. Both molecular and biochemical parameter-based clustering showed that interspecific hybrids exhibit transgressive segregation with increased antioxidants that help alleviate the health problems. Novelty and scientific contribution: These newly developed pummelo × sweet orange citrus hybrids are a valuable source of high-quality antioxidants for a healthy diet. The identification of trait markers that enable selection at the seedling stage is of great benefit to citrus breeders, as the characteristic features of a mature tree are not yet visible at the juvenile stage.

A rare case of complicated malaria presenting as warm autoimmune hemolytic anemia.

Autoimmune hemolytic anemia (AIHA) has been rarely reported worldwide or from India as the underlying cause of anemia in malaria. We hereby present a case of complicated Plasmodium falciparum malaria with concomitant warm AIHA in a 31-year-old male. Direct Antiglobulin Test (DAT) was positive and elution studies showed pan-agglutination reaction. Clinico-hematological and serological follow-up of the patient was done post artesunate treatment until day 9. We suggest that it is important to establish the immune basis of anemia in malaria patients for guiding the treatment plan for the clinicians and providing packed red blood cell transfusion if required.

Functional interaction between ELL transcription elongation factor and Epe1 reveals the role of Epe1 in the regulation of transcription outside heterochromatin.

Eleven-nineteen lysine-rich leukemia (ELL) is a eukaryotic RNA polymerase II transcription elongation factor. In Schizosaccharomyces pombe, it is important for survival under genotoxic stress conditions. However, the molecular basis underlying this function of ELL in S. pombe is yet to be deciphered. Here, we carried out a genetic screen to identify multicopy suppressor(s) that could restore normal growth of ell1 deletion mutant in the presence of DNA damaging agent. Sequence analysis of the identified suppressors revealed the anti-silencing protein, Epe1, as one of the suppressors of ell1 deletion associated genotoxic stress sensitivity. Our results further demonstrate that the overexpression of Epe1 could suppress all other phenotypes associated with the absence of Ell1. Moreover, transcriptional defect of ell1Δ strain could also be alleviated by the overexpression of Epe1. Epe1 also showed a physical interaction with Ell1. Interestingly, we also observed that the region of Epe1 encompassing 403-948 amino acids was indispensable for all the above functions. Furthermore, our results show that the overexpression of Epe1 causes increased H3K9 acetylation and RNA polymerase II recruitment. Taken together, our results show a functional interaction between Epe1 and Ell1, and this function is independent of the well-known JmjC and N-terminal transcriptional activation domains of Epe1 in S. pombe.

Sequence, structural and functional conservation among the human and fission yeast ELL and EAF transcription elongation factors.

BACKGROUND: Transcription elongation is a dynamic and tightly regulated step of gene expression in eukaryotic cells. Eleven nineteen Lysine rich Leukemia (ELL) and ELL Associated Factors (EAF) family of conserved proteins are required for efficient RNA polymerase II-mediated transcription elongation. Orthologs of these proteins have been identified in different organisms, including fission yeast and humans. METHODS AND RESULTS: In the present study, we have examined the sequence, structural and functional conservation between the fission yeast and human ELL and EAF orthologs. Our computational analysis revealed that these proteins share some sequence characteristics, and were predominantly disordered in both organisms. Our functional complementation assays revealed that both human ELL and EAF proteins could complement the lack of ell1+ or eaf1+ in Schizosaccharomyces pombe respectively. Furthermore, our domain mapping experiments demonstrated that both the amino and carboxyl terminal domains of human EAF proteins could functionally complement the S. pombe eaf1 deletion phenotypes. However, only the carboxyl-terminus domain of human ELL was able to partially rescue the phenotypes associated with lack of ell1+ in S. pombe. CONCLUSIONS: Collectively, our work adds ELL-EAF to the increasing list of human-yeast complementation gene pairs, wherein the simpler fission yeast can be used to further enhance our understanding of the role of these proteins in transcription elongation and human disease.

Absence of the Rpb9 subunit of RNA polymerase II reduces the chronological life span in fission yeast.

Fission yeast RNA polymerase II consists of 12 subunits, Rpb1-Rpb12. Among these subunits, Rpb9 is the only subunit whose absence does not cause lethality under optimum growth conditions in fission yeast. However, an rpb9 null fission yeast mutant exhibits a slow-growth phenotype under optimum growth conditions and a defect in survival under environmental and genotoxic stress conditions. To further gain an understanding of its physiological roles, in the present study we have elucidated the role of the Rpb9 subunit in chronological aging using fission yeast as the model organism. Our results provide evidence that the absence of Rpb9 reduces the chronological life span in fission yeast. Our data further shows that lack of Rpb9 in fission yeast causes oxidative stress sensitivity and accumulation of reactive oxygen species during the stationary phase. Our domain mapping experiments have demonstrated that the Rpb9 region encompassing its amino-terminal zinc finger domain and the central linker region is important for the role of Rpb9 in chronological aging. Finally, we also show that expression of the budding yeast or human Rpb9 ortholog can functionally complement the reduced chronological life span phenotype of the fission yeast rpb9 deletion mutant. Taken together, our study has identified a new role of the Rpb9 subunit in chronological aging.

Arabidopsis thaliana possesses two novel ELL associated factor homologs.

Transcription elongation is one of the key steps at which RNA polymerase II-directed expression of protein-coding genes is regulated in eukaryotic cells. Different proteins have been shown to control this process, including the ELL/EAF family. ELL Associated Factors (EAFs) were first discovered in a yeast two-hybrid screen as interaction partners of the human ELL (Eleven nineteen Lysine-rich Leukemia) transcription elongation factor. Subsequently, they have been identified in different organisms, including Schizosaccharomyces pombe. However, no homolog(s) of EAF has as yet been characterized from plants. In the present work, we identified EAF orthologous sequences in different plants and have characterized two novel Arabidopsis thaliana EAF homologs, AtEAF-1 (At1g71080) and AtEAF-2 (At5g38050). Sequence analysis showed that both AtEAF-1 and AtEAF-2 exhibit similarity with its S. pombe EAF counterpart. Moreover, both Arabidopsis thaliana and S. pombe EAF orthologs share conserved sequence characteristic features. Computational tools also predicted a high degree of disorder in regions towards the carboxyl terminus of these EAF proteins. We demonstrate that AtEAF-2, but not AtEAF-1 functionally complements growth deficiencies of Schizosaccharomyces pombe eaf mutant. We also show that only AtEAF-1 displays transactivation potential resembling the S. pombe EAF ortholog. Subsequent expression analysis in A. thaliana showed that both homologs were expressed at varying levels during different developmental stages and in different tissues tested in the study. Individual null-mutants of either AtEAF-1 or AtEAF-2 are developmentally normal implying their functional redundancy. Taken together, our results provide first evidence that A. thaliana also possesses functional EAF proteins, suggesting an evolutionary conservation of these proteins across organisms.

Schizosaccharomyces pombe Pol II transcription elongation factor ELL functions as part of a rudimentary super elongation complex.

ELL family transcription factors activate the overall rate of RNA polymerase II (Pol II) transcription elongation by binding directly to Pol II and suppressing its tendency to pause. In metazoa, ELL regulates Pol II transcription elongation as part of a large multisubunit complex referred to as the Super Elongation Complex (SEC), which includes P-TEFb and EAF, AF9 or ENL, and an AFF family protein. Although orthologs of ELL and EAF have been identified in lower eukaryotes including Schizosaccharomyces pombe, it has been unclear whether SEC-like complexes function in lower eukaryotes. In this report, we describe isolation from S. pombe of an ELL-containing complex with features of a rudimentary SEC. This complex includes S. pombe Ell1, Eaf1, and a previously uncharacterized protein we designate Ell1 binding protein 1 (Ebp1), which is distantly related to metazoan AFF family members. Like the metazoan SEC, this S. pombe ELL complex appears to function broadly in Pol II transcription. Interestingly, it appears to have a particularly important role in regulating genes involved in cell separation.

Comparative RNA sequencing based transcriptome profiling of regular bearing and alternate bearing mango (Mangifera indica L.) varieties reveals novel insights into the regulatory mechanisms underlying alternate bearing.

OBJECTIVE: This study is to understand a comprehensive perspective on the molecular mechanisms underlying alternate bearing in mango (Mangifera indica L.) via transcriptome wide gene expression profiling of both regular and irregular mango varieties. RESULTS: Transcriptome data of regular (Neelam) and irregular (Dashehari) mango varieties revealed a total of 42,397 genes. Out of that 12,557 significantly differentially expressed genes were identified, of which 6453 were found to be up-regulated and 6104 were found to be down-regulated genes. Further, many of the common unigenes which were involved in hormonal regulation, metabolic processes, oxidative stress, ion homeostasis, alternate bearing etc. showed significant differences between these two different bearing habit varieties. Pathway analysis showed the highest numbers of differentially expressed genes were related with the metabolic processes (523). A total of 26 alternate bearing genes were identified and principally three genes viz; SPL-like gene (GBVX01015803.1), Rumani GA-20-oxidase-like gene (GBVX01019650.1) and LOC103420644 (GBVX01016070.1) were significantly differentially expressed (at log2FC and pval less than 0.05) while, only single gene (gbGBVW01004309.1) related with flowering was found to be differentially expressed. A total of 15 differentially expressed genes from three important pathways viz; alternate bearing, carbohydrate metabolism and hormone synthesis were validated using Real time PCR and results were at par with in silico analysis. CONCLUSIONS: Deciphering the differentially expressed genes (DEGs) and potential candidate genes associated with alternate bearing, hormone and carbohydrate metabolism pathways will help for illustrating the molecular mechanisms underlying the bearing tendencies in mango.

Genome-wide transcriptional response to altered levels of the Rpb7 subunit of RNA polymerase II identifies its role in DNA damage response in Schizosaccharomyces pombe.

Transcription of protein-coding genes is a highly regulated process. In eukaryotes, it involves cross-talk between the RNA polymerase II enzyme and different proteins of the transcriptional machinery. Twelve different subunits, Rpb1 to Rpb12, constitute RNA polymerase II. The sequence of the Rpb7 subunit is highly conserved across organisms. However, our knowledge and understanding of the role of Rpb7 in Schizosaccharomyces pombe is still limited. Therefore, in the present study we have studied the transcriptional response of S. pombe cells expressing reduced levels of rpb7+. Our global transcriptional analysis revealed that expression of genes belonging to different DNA repair pathways was downregulated by reduced rpb7+ expression. It was observed that survival of S. pombe cells expressing low rpb7+ levels was compromised under genotoxic stress conditions. Rpb7 also exhibited genetic interaction with genes of various DNA repair pathways. Furthermore, the growth sensitivity of S. pombe cells with low rpb7+ levels under DNA-damaging conditions was completely rescued by human Rpb7, indicating a functional conservation between these proteins. In summary, results from our whole-genome level gene expression analysis, as well as phenotypic and genetic experiments suggest a role for Rpb7 in DNA damage response in S. pombe.

The amino-terminal domain of ELL transcription elongation factor is essential for ELL function in Schizosaccharomyces pombe.

Transcriptional elongation is a critical step for regulating expression of protein-coding genes. Multiple transcription elongation factors have been identified in vitro, but the physiological roles of many of them are still not clearly understood. The ELL (Eleven nineteen Lysine rich Leukemia) family of transcription elongation factors are conserved from fission yeast to humans. Schizosaccharomyces pombe contains a single ELL homolog (SpELL) that is not essential for its survival. Therefore to gain insights into the in vivo cellular functions of SpELL, we identified phenotypes associated with deletion of ell1 in S. pombe. Our results demonstrate that SpELL is required for normal growth of S. pombe cells. Furthermore, cells lacking ell1+ exhibit a decrease in survival when exposed to DNA-damaging conditions, but their growth is not affected under environmental stress conditions. ELL orthologs in different organisms contain three conserved domains, an amino-terminal domain, a middle domain and a carboxyl-terminal domain. We also carried out an in vivo functional mapping of these conserved domains within S. pombe ELL and uncovered a critical role for its amino-terminus in regulating all its cellular functions, including growth under different conditions, transcriptional elongation potential and interaction with S. pombe EAF. Taken together our results suggest that the domain organization of ELL proteins is conserved across species, but the in vivo functions as well as the relationship between the various domains and roles of ELL show species-specific differences.

Regulation of RNA polymerase II-mediated transcriptional elongation: Implications in human disease.

Expression of protein-coding genes is primarily regulated at the level of transcription. Most of the earlier studies focussed on understanding the assembly of the pre-initiation complex at the promoter of genes and subsequent initiation of transcription as the regulatory steps in transcription. However, research over the last decade has demonstrated the significance of regulating transcription of genes at the elongation stage. Several new proteins have been identified that control this step and our knowledge about their functions is expanding rapidly. Moreover, an increasing body of evidence suggests that a dysfunction of these transcription elongation factors is related to several diseases. Here, we review the latest advances in our understanding about the in vivo roles of the transcription elongation factors and their link with diseases. © 2016 IUBMB Life, 68(9):709-716, 2016.

Challenges in the diagnosis and management of autoimmune hemolytic anemia: A case-based approach. Experience from a tertiary care hospital in the Haryana region.

BACKGROUND: Autoimmune hemolytic anemia (AIHA) is a rare immune disorder which occurs when antibodies are directed against self red blood cells (RBCs) leading to hemolysis. AIHA is widely classified as warm autoimmune hemolytic anemia, cold agglutinin syndrome, mixed AIHA, paroxysmal cold hemoglobinuria and rarely drug induced AIHA. The pathogenesis of AIHA is complex interplay between genetic predisposition, immune dysregulation and enviornmental triggers. A direct antiglobulin test can be used to assess the immunological origin of the hemolysis in order to diagnose AIHA after identifying laboratory and clinical symptoms of hemolysis. OBJECTIVE: The objective is to understand underlying mechanism in AIHAs, and usage of targeted therapies to modulate specific components of the immune response. MATERIALS AND METHODS: We are hereby presenting a case series of 11 clinically suspected cases of AIHA in collaboration with their clinical features, immuno-hematological and other laboratory parameters, Flow cytometric analysis of lymphocyte subset in relevant cases, underlying etiology as well as serological subtype are also included. RESULTS: Majority of the patients were categorized as secondary AIHA (7/11, 63.63%). Out of 11 cases 7 were serologically subtyped as warm AIHA (7/11, 63.63%) ,2 cases were DaaT negative AIHA (2/11;18.18%), 2 cases were characterized as mixed AIHA subtype (2/11, 18.18%). CONCLUSION: Accurate subtyping of AIHA requires a systematic immunohematological approach coupled with comprehensive evaluations of clinical, hematological, and biochemical parameters.

Use of quantitative membrane proteomics identifies a novel role of mitochondria in healing injured muscles.

Skeletal muscles are proficient at healing from a variety of injuries. Healing occurs in two phases, early and late phase. Early phase involves healing the injured sarcolemma and restricting the spread of damage to the injured myofiber. Late phase of healing occurs a few days postinjury and involves interaction of injured myofibers with regenerative and inflammatory cells. Of the two phases, cellular and molecular processes involved in the early phase of healing are poorly understood. We have implemented an improved sarcolemmal proteomics approach together with in vivo labeling of proteins with modified amino acids in mice to study acute changes in the sarcolemmal proteome in early phase of myofiber injury. We find that a notable early phase response to muscle injury is an increased association of mitochondria with the injured sarcolemma. Real-time imaging of live myofibers during injury demonstrated that the increased association of mitochondria with the injured sarcolemma involves translocation of mitochondria to the site of injury, a response that is lacking in cultured myoblasts. Inhibiting mitochondrial function at the time of injury inhibited healing of the injured myofibers. This identifies a novel role of mitochondria in the early phase of healing injured myofibers.

Rpb4 and Rpb7: multifunctional subunits of RNA polymerase II.

The 12-subunit RNA polymerase II enzyme in yeasts and higher eukaryotic cells is important for transcription of protein-coding genes. Its fourth and seventh largest subunits named Rpb4 and Rpb7, respectively, display some unique features that distinguish them from the remaining subunits of this enzyme. These two subunits also bind to each other forming a complex in archaebacteria, yeasts, plants and humans. Our knowledge about the structure and functions of this complex has greatly advanced in recent years. These subunits were initially considered to be important only for initiation of transcription and stress response. However, recent evidence suggests that they are not only involved in transcription, but also in DNA repair, mRNA export and decay as well as translation, highlighting the roles of this heterodimer in diverse biological processes. In this article, we review the current status of these two subunits and discuss attributes of their structure and function across organisms.

Differential gene expression associated with flower development of mango (Mangifera indica L.) varieties with different shelf-life.

Mango (Mangifera indica L.) is one of the most important commercial fruit crop grown in many parts of the world. Major challenges affecting mango trade are short shelf-life, high susceptibility to chilling injury, post-harvest diseases and consumer demand for improved fruit quality. The objective of the present study was to reveal the key regulators present in bud and flower tissues during flower development stage, associated with fruit development and affect the shelf-life of the mango fruit. RNA-sequencing of contrasting genotypes having short and long shelf-life, was carried out. Comparative differential expression pathway studies of long shelf-life (Totapuri) and short shelf-life (Bombay Green) mango genotypes revealed a total of 177 highly differentially expressed genes. Out of 177 total genes, 101 genes from endoplasmic reticulum pathway and very few from gibberellins (3) and jasmonic acid (1) pathway were identified. Genes from endoplasmic reticulum pathway like hsp 90, SRC2, DFRA, CHS, BG3 and ASPG1 mainly up regulated in Bombay Green. Uniprotein B9R8D3 also shows up regulation in Bombay Green. Ethylene insensitive pathway gene EIL1 up regulated in Bombay Green. Gene CAD1 from phenylpropanoid pathway mainly up regulated in Bombay Green. A total of 4 SSRs and 227 SNPs were mined from these pathways specific to the shelf-life. Molecular studies of endoplasmic reticulum, phenylpropanoid, ethylene, polygalacturonase and hormone pathways at the time of bud and flower formation revealed key regulators that determine the shelf-life of mango fruit.

Rootstock-mediated carbohydrate metabolism, nutrient contents, and physiological modifications in regular and alternate mango (Mangifera indica L.) scion varieties.

Most of the popular scion varieties of mango possess alternate/irregular bearing. There are many external and internal factors assigned, among them carbohydrate reserves, and nutrient content plays important roles in the floral induction process in many crop species. In addition to that rootstock can alter the carbohydrate reserve and nutrient acquisition of scion varieties in fruit crops. The present investigation was carried out to understand the effect of rootstocks on the physiochemical traits of leaf, and bud and nutrient content in regular and alternate bearing varieties of mango. The rootstock "Kurukkan" promoted starch content in leaves of both alternate bearing varieties 'Dashehari' (5.62 mg/g) and regular 'Amrapali' (5.49 mg/g) and encouraged higher protein content (6.71 mg/g) and C/N ratio (37.94) in buds of alternate bearing 'Dashehari'. While Olour rootstock upregulated the reducing sugar in leaves of 'Amrapali' (43.56 mg/g) and promoted K (1.34%) and B (78.58 ppm) content in reproductive buds of 'Dashehari'. Stomatal density in 'Dashehari' scion variety was found higher on Olour rootstock (700.40/mm 2), while the rootstock fails to modify stomatal density in the scion variety regular bearer 'Amrapali'. Further, a total of 30 carbohydrate metabolism-specific primers were designed and validated in 15 scion/rootstock combinations. A total of 33 alleles were amplified among carbohydrate metabolism-specific markers, which varied from 2 to 3 alleles with a mean of 2.53 per locus. Maximum and minimum PIC value was found for NMSPS10, and NMTPS9 primers (0.58). Cluster analysis revealed that scion grafted on Kurukkan rootstock clustered together except 'Pusa Arunima' on Olour rootstock. Our analysis revealed that Fe is the key component that is commonly expressed in both leaf and bud. Although Stomatal density (SD) and Intercellular CO2 Concentration (Ci) are more specific to leaf and Fe, B, and total sugar (TS) are abundant in buds. Based on the results it can be inferred that the physiochemical and nutrient responses of mango scion varieties are manipulated by the rootstock, hence, the scion-rootstock combination can be an important consideration in mango for selecting suitable rootstock for alternate/irregular bearer varieties.

Harvesting Maturity Assessment of Newly Developed Citrus Hybrids (Citrus maxima Merr. × Citrus sinensis (L.) Osbeck) for Optimum Juice Quality.

The assessment of the optimum harvesting stage is a prerequisite to evaluating the performance of new citrus genotypes. The intrinsic and extrinsic fruit quality traits of citrus fruits change throughout their developmental process; therefore, to ensure the highest quality, the fruit must be harvested at an appropriate stage of maturity. The biochemical changes in terms of total soluble solids (TSS), titratable acidity (TA), TSS/TA ratio, BrimA (Brix minus acidity), and ascorbic acid, in addition to the organoleptic acceptability of 16 new interspecific citrus hybrids, were evaluated in New Delhi (India) during the H1-H8 harvesting stage at 15-day intervals to standardize the optimum harvesting stage. The TA and ascorbic acid content were at a maximum level during the early harvesting stage and declined with time, reaching the minimum level in the last harvesting stage. The TSS, TSS/TA ratio, and BrimA values were found to have an increasing trend up to the last stage in most of the hybrids. The juice content shows an inclining trend during the initial harvesting observations, followed by stable juice content and then a decline. The BrimA was found to be a better predictor for consumer acceptability compared to the traditional maturity index TSS/TA ratio and, thus, harvesting maturity. Specific TSS, TA, and BrimA values, in addition to the juice percentage and ascorbic acid content, corresponding to the highest hedonic score, were judged as the optimum harvesting stage indicators for an individual hybrid genotype. Among the interspecific hybrids, SCSH-9-10/12, SCSH-11-15/12, and SCSH-17-19/13 were found to be superior, having better juice acceptability organoleptic scores (≥6.0) and higher juice content (≥40%). Principal component analysis based on fruit physico-chemical traits could be able to distinguish the optimum maturity stage in all of the citrus genotypes.

Practical considerations for a TB controlled human infection model (TB-CHIM); the case for TB-CHIM in Africa, a systematic review of the literature and report of 2 workshop discussions in UK and Malawi.

Background: Tuberculosis (TB) remains a major challenge in many domains including diagnosis, pathogenesis, prevention, treatment, drug resistance and long-term protection of the public health by vaccination. A controlled human infection model (CHIM) could potentially facilitate breakthroughs in each of these domains but has so far been considered impossible owing to technical and safety concerns. Methods: A systematic review of mycobacterial human challenge studies was carried out to evaluate progress to date, best possible ways forward and challenges to be overcome. We searched MEDLINE (1946 to current) and CINAHL (1984 to current) databases; and Google Scholar to search citations in selected manuscripts. The final search was conducted 3 rd February 2022. Inclusion criteria: adults ≥18 years old; administration of live mycobacteria; and interventional trials or cohort studies with immune and/or microbiological endpoints. Exclusion criteria: animal studies; studies with no primary data; no administration of live mycobacteria; retrospective cohort studies; case-series; and case-reports. Relevant tools (Cochrane Collaboration for RCTs and Newcastle-Ottawa Scale for non-randomised studies) were used to assess risk of bias and present a narrative synthesis of our findings. Results: The search identified 1,388 titles for review; of these 90 were reviewed for inclusion; and 27 were included. Of these, 15 were randomised controlled trials and 12 were prospective cohort studies. We focussed on administration route, challenge agent and dose administered for data extraction. Overall, BCG studies including fluorescent BCG show the most immediate utility, and genetically modified Mycobacteria tuberculosis is the most tantalising prospect of discovery breakthrough. Conclusions: The TB-CHIM development group met in 2019 and 2022 to consider the results of the systematic review, to hear presentations from many of the senior authors whose work had been reviewed and to consider best ways forward. This paper reports both the systematic review and the deliberations. Registration: PROSPERO ( CRD42022302785; 21 January 2022).

High resolution mapping of QTLs for fruit color and firmness in Amrapali/Sensation mango hybrids.

Introduction: Mango (Mangifera indica L.), acclaimed as the 'king of fruits' in the tropical world, has historical, religious, and economic values. It is grown commercially in more than 100 countries, and fresh mango world trade accounts for ~3,200 million US dollars for the year 2020. Mango is widely cultivated in sub-tropical and tropical regions of the world, with India, China, and Thailand being the top three producers. Mango fruit is adored for its taste, color, flavor, and aroma. Fruit color and firmness are important fruit quality traits for consumer acceptance, but their genetics is poorly understood. Methods: For mapping of fruit color and firmness, mango varieties Amrapali and Sensation, having contrasting fruit quality traits, were crossed for the development of a mapping population. Ninety-two bi-parental progenies obtained from this cross were used for the construction of a high-density linkage map and identification of QTLs. Genotyping was carried out using an 80K SNP chip array. Results and discussion: Initially, we constructed two high-density linkage maps based on the segregation of female and male parents. A female map with 3,213 SNPs and male map with 1,781 SNPs were distributed on 20 linkages groups covering map lengths of 2,844.39 and 2,684.22cM, respectively. Finally, the integrated map was constructed comprised of 4,361 SNP markers distributed on 20 linkage groups, which consisted of the chromosome haploid number in Mangifera indica (n =20). The integrated genetic map covered the entire genome of Mangifera indica cv. Dashehari, with a total genetic distance of 2,982.75 cM and an average distance between markers of 0.68 cM. The length of LGs varied from 85.78 to 218.28 cM, with a mean size of 149.14 cM. Phenotyping for fruit color and firmness traits was done for two consecutive seasons. We identified important consistent QTLs for 12 out of 20 traits, with integrated genetic linkages having significant LOD scores in at least one season. Important consistent QTLs for fruit peel color are located at Chr 3 and 18, and firmness on Chr 11 and 20. The QTLs mapped in this study would be useful in the marker-assisted breeding of mango for improved efficiency.