Null Locus Research Articles

Molecular characteristics of Neisseria meningitidis carriage strains in university students in Lithuania

BackgroundNeisseria meningitidis can be carried asymptomatically in the human oropharynx without causing symptoms. Meningococcal carriage is relevant to the epidemiology of invasive meningococcal disease (IMD). No carriage studies have been performed among the general population in Lithuania, whereas the incidence of IMD in Lithuania was among the highest in European countries from 2009 to 2019.ResultsWe analyzed a total of 401 oropharyngeal samples collected from university students from December 2021 to February 2023 for N. meningitidis carriage using direct swab PCR assays and culture. The overall carriage prevalence based on both or either swab PCR or culture was 4.99%. PCR-based assays were used to characterize 15 carriage isolates, including detection of genogroup, multilocus sequence typing profile, and typing of antigens PorA and FetA. The most common carriage isolates were capsule null locus (cnl), accounting for 46.7%, followed by genogroups B (26.7%) and Y (13.3%). We also performed a molecular characterization of invasive N. meningitidis isolates collected during the COVID-19 pandemic and post-pandemic period to understand better the meningococcal carriage in the context of prevailing invasive strains. Despite the substantial decrease in the incidence of IMD during the 2020–2022 period, clonal complex 32 (CC32) of serogroup B continued to be the most prevalent IMD-causing CC in Lithuania. However, CC32 was not detected among carriage isolates. The most common CCs were CC269, CC198, and CC1136. The antigen peptide variants found in most carried isolates were classified as ‘insufficient data’ according to the MenDeVAR Index to evaluate the potential coverage by the 4CMenB vaccine. Nearly half of the isolates were potentially covered by the Men-Fhbp vaccine. Resistance to ciprofloxacin was detected only for one cnl isolate. All isolates were susceptible to penicillin and ceftriaxone. Our analysis identified frequent partying (≥ 4 times/month) as a risk factor for meningococcal carriage, whereas smoking, living in a dormitory, and previous COVID-19 illness were not associated with the carriage.ConclusionsOur study revealed a low prevalence of meningococcal carriage among university students in Lithuania. The carriage isolates showed genetic diversity, although almost half of them were identified as having a null capsule locus.

Prevalence and persistence of Neisseria meningitidis carriage in Swedish university students.

The bacterium Neisseria meningitidis causes life-threatening disease worldwide, typically with a clinical presentation of sepsis or meningitis, but can be carried asymptomatically as part of the normal human oropharyngeal microbiota. The aim of this study was to examine N. meningitidis carriage with regard to prevalence, risk factors for carriage, distribution of meningococcal lineages and persistence of meningococcal carriage. Throat samples and data from a self-reported questionnaire were obtained from 2744 university students (median age: 23 years) at a university in Sweden on four occasions during a 12-month period. Meningococcal isolates were characterised using whole-genome sequencing. The carriage rate among the students was 9.1% (319/3488; 95% CI 8.2-10.1). Factors associated with higher carriage rate were age ≤22 years, previous tonsillectomy, cigarette smoking, drinking alcohol and attending parties, pubs and clubs. Female gender and sharing a household with children aged 0-9 years were associated with lower carriage. The most frequent genogroups were capsule null locus (cnl), group B and group Y and the most commonly identified clonal complexes (cc) were cc198 and cc23. Persistent carriage with the same meningococcal strain for 12 months was observed in two students. Follow-up times exceeding 12 months are recommended for future studies investigating long-term carriage of N. meningitidis.

The codimension 2 null cut locus with applications to spacetime topology

In this paper, we review and extend some results in the literature pertaining to spacetime topology while naturally utilizing properties of the codimension 2 null cut locus. Our results fall into two classes, depending on whether or not one assumes the presence of horizons. Included among the spacetimes we consider are those that apply to the asymptotically (locally) anti-de sitter (AdS) setting.

Characterization of null cones under a Ricci curvature condition

We study conditions under which a totally umbilic immersed null hypersurface in a Lorentzian manifold is contained in a null cone. The main tool used for this purpose is the rigging technique and the analysis of the Raychaudhuri equation for an immersed null hypersurface. As an application, conditions to ensure that the null conjugate locus is a single point and the existence of two vertices in a null cone are also given.

420. Prevalence of Oropharyngeal Meningococcal Carriage in an Urban STD Clinic

Background Neisseria meningitidis (Nm) can cause invasive disease, but it also asymptomatically colonizes the pharynx in approximately 10% of the general population. Older studies have reported higher carriage rates (>30%) among individuals attending sexually transmitted disease (STD) clinics. This study examined the prevalence of oropharyngeal Nm carriage in STD clinic attendees in Columbus, Ohio.MethodsPer normal procedures, all patients presenting for care in the STD clinic who report oral sex in the last year are screened for oropharyngeal Neisseria gonorrhoeae (Ng) using nucleic acid amplification testing (NAAT). For the same patients, we also initiate cultures using media selective for Neisseria spp. Analytical Profile Index Neisseria-Haemophilus (API NH) and Nm-specific PCR screening is performed on colonies with oxidase-positive Gram-negative diplococci to distinguish between Ng and Nm. For this study, we then performed PCR-based genogrouping on confirmed Nm isolates.ResultsBetween July 2018 and March 2019, oropharyngeal screening occurred at 5,015 patient visits and oropharyngeal Nm was detected at 163 visits (3.3%). Nm-positive individuals were primarily male (69.9%), Caucasian (62.6%), with non-Hispanic ethnicity (98.8%). The median age was 27 years and 5.5% were HIV-positive. Among male cases, 49.1% reported sex with men; among women, 98.0% reported sex with men. Meningococcal vaccination status was unknown for 71.2%, but 26.4% had documentation of prior MenACWY vaccination and 2.3% had prior MenB vaccination. Among the 163 cases, genogroup distribution was 23.9% B, 10.4% E, 9.8% Z, 3.1% C, 0.0% W, 0.0% Y, and 39.3% capsule null locus. For 13.5%, the selected screening approach could not determine genogroup.ConclusionIn STD clinic patients reporting recent oral sex, we found a much lower prevalence of oropharyngeal Nm carriage compared with what has been reported historically for similar populations. While NmB was the most common capsular type identified by genogrouping, almost 40% of Nm isolates contained the capsule null locus, making them unable to express capsule. Additional studies should evaluate the effect of Nm vaccination programs on carriage among STD-clinic attendees.Disclosures All authors: No reported disclosures.

Carriage meningococcal isolates with capsule null locus dominate among high school students in a non-endemic period, Italy, 2012–2013

Meningococcal disease incidence in Italy remains quite low in the overall population except for infants. Within a study on carriage isolates among high school students we aimed to define: i) the prevalence of carriage isolates, ii) the phenotypic and iii) the molecular features of meningococci by Whole Genome Sequencing (WGS).A total of 1697 pharyngeal samples from undergraduate students (age range 14–19 years) were collected from 2012 to 2013 from six larger cities in Italy. One hundred and twenty culture positive meningococci (7%) were analyzed. Carriage isolates were sent to the National Reference Laboratory for invasive meningococcal disease (IMD) for PCR-based serogroup identification, Multilocus Sequence Typing, PorA and FetA typing. Moreover, factor H binding protein (fHbp), Neisseria Heparin Binding Antigen (NHBA) and Neisserial adhesin A (NadA) were typed. Core genome MLST (cgMLST) was performed on a subsample of 75 carriage isolates.Capsule null locus (cnl) predominated (47%), followed by serogroup B (27%). The antimicrobial susceptibility profile revealed an high prevalence of reduced susceptibility to penicillin G (54%) and a full susceptibility to ceftriaxone, ciprofloxacin and rifampicin. Carriage isolates presented a high genetic diversity: the clonal complexes (ccs) cc1136, cc198 and cc41/44, were the predominant. An high heterogeneity was also observed for PorA and FetA types. The fhbp and nhba genes were identified in all the carriage isolates; only 5% of the carriage isolates presented the nadA gene. The core genome MLST analysis revealed that the majority of the cnl isolates clustered in a distinct group.The evidence gathered during this study provides the estimate of carriage isolates in high school students in a non-epidemic period in Italy that was lower than expected. Moreover, the highest proportion of carriage isolates were cnl and, overall, they were molecular heterogeneous.

Acquisition of the capsule locus by horizontal gene transfer in Neisseria meningitidis is often accompanied by the loss of UDP-GalNAc synthesis

Pathogenic meningococci have acquired a 24 kb capsule synthesis island (cps) by horizontal gene transfer which consists of a synthetic locus and associated capsule transport genes flanked by repetitive Regions D and D’. Regions D and D’ contain an intact gene encoding a UDP-galactose epimerase (galE1) and a truncated remnant (galE2), respectively. In this study, GalE protein alleles were shown to be either mono-functional, synthesising UDP-galactose (UDP-Gal), or bi-functional, synthesising UDP-Gal and UDP-galactosamine (UDP-GalNAc). Meningococci possessing a capsule null locus (cnl) typically possessed a single bi-functional galE. Separation of functionality between galE1 and galE2 alleles in meningococcal isolates was retained for all serogroups except serogroup E which has a synthetic requirement for UDP-GalNAc. The truncated galE2 remnant in Region D’ was also phylogenetically related to the bi-functional galE of the cnl locus suggesting common ancestry. A model is proposed in which the illegitimate recombination of the cps island into the galE allele of the cnl locus results in the formation of Region D’ containing the truncated galE2 locus and the capture of the cps island en bloc. The retention of the duplicated Regions D and D’ enables inversion of the synthetic locus within the cps island during bacterial growth.

Molecular characterization of invasive capsule null Neisseria meningitidis in South Africa

BackgroundThe meningococcal capsule is an important virulence determinant. Unencapsulated meningococci lacking capsule biosynthesis genes and containing the capsule null locus (cnl) are predominantly non-pathogenic. Rare cases of invasive meningococcal disease caused by cnl isolates belonging to sequence types (ST) and clonal complexes (cc) ST-845 (cc845), ST-198 (cc198), ST-192 (cc192) and ST-53 (cc53) have been documented. The clinical significance of these isolates however remains unclear. We identified four invasive cnl meningococci through laboratory-based surveillance in South Africa from 2003 through 2013, which we aimed to characterize using whole genome data.ResultsOne isolate [NG: P1.7-2,30: F1-2: ST-53 (cc53)] contained cnl allele 12, and caused empyema in an adult male with bronchiectasis from tuberculosis, diabetes mellitus and a smoking history. Three isolates were NG: P1.18-11,42-2: FΔ: ST-192 (cc192) and contained cnl allele 2. One patient was an adolescent male with meningitis. The remaining two isolates were from recurrent disease episodes (8 months apart) in a male child with deficiency of the sixth complement component, and with the exception of two single nucleotide polymorphisms, contained identical core genomes. The ST-53 (cc53) isolate possessed alleles for NHBA peptide 191 and fHbp variant 2; whilst the ST-192 (cc192) isolates contained NHBA peptide 704 and fHbp variant 3. All four isolates lacked nadA. Comparison of the South African genomes to 61 additional cnl genomes on the PubMLST Neisseria database (http://pubmlst.org/neisseria/), determined that most putative virulence genes could be found in both invasive and carriage phenotypes.ConclusionsAlthough rare, invasive disease by cnl meningococci may be associated with host immunodeficiency and such patients may benefit from protein-based meningococcal vaccines.

Leishmania HASP and SHERP Genes Are Required for In Vivo Differentiation, Parasite Transmission and Virulence Attenuation in the Host.

Differentiation of extracellular Leishmania promastigotes within their sand fly vector, termed metacyclogenesis, is considered to be essential for parasites to regain mammalian host infectivity. Metacyclogenesis is accompanied by changes in the local parasite environment, including secretion of complex glycoconjugates within the promastigote secretory gel and colonization and degradation of the sand fly stomodeal valve. Deletion of the stage-regulated HASP and SHERP genes on chromosome 23 of Leishmania major is known to stall metacyclogenesis in the sand fly but not in in vitro culture. Here, parasite mutants deficient in specific genes within the HASP/SHERP chromosomal region have been used to investigate their role in metacyclogenesis, parasite transmission and establishment of infection. Metacyclogenesis was stalled in HASP/SHERP mutants in vivo and, although still capable of osmotaxis, these mutants failed to secrete promastigote secretory gel, correlating with a lack of parasite accumulation in the thoracic midgut and failure to colonise the stomodeal valve. These defects prevented parasite transmission to a new mammalian host. Sand fly midgut homogenates modulated parasite behaviour in vitro, suggesting a role for molecular interactions between parasite and vector in Leishmania development within the sand fly. For the first time, stage-regulated expression of the small HASPA proteins in Leishmania (Leishmania) has been demonstrated: HASPA2 is expressed only in extracellular promastigotes and HASPA1 only in intracellular amastigotes. Despite its lack of expression in amastigotes, replacement of HASPA2 into the null locus background delays onset of pathology in BALB/c mice. This HASPA2-dependent effect is reversed by HASPA1 gene addition, suggesting that the HASPAs may have a role in host immunomodulation.

The augmented base locus of real divisors over arbitrary fields

We show that the augmented base locus coincides with the exceptional locus (i.e., null locus) for any nef $$\mathbb R$$ -Cartier divisor on any scheme projective over a field (of any characteristic). Next we prove a semi-ampleness criterion in terms of the exceptional locus generalizing a result of Keel. We also discuss some problems related to augmented base loci of log divisors.

Phylogenetic study of clonal complex (CC)198 capsule null locus (cnl) genomes: A distinctive group within the species Neisseria meningitidis

Capsule null locus (cnl) strains, one type of specific unencapsulated Neisseria spp., only have regions D and E of the capsule gene cluster which encodes the genes for capsule biosynthesis, modification, and transportation. Compared with encapsulated strains, regions A and C of cnl strains have been replaced by 113 or 114bp conserved non-coding sequences. Cnl strains include multiple clonal complexes (CC). According to previous studies, CC198 is the major clonal lineage in both cnl patients and healthy cnl carriers. We hypothesized that CC198 possesses different genome characteristics compared with other cnl strains. In this study, we obtained the draft genomes of two CC198 strains from healthy carriers. Using 75071 single nucleotide polymorphisms located in 1163 core genes, we constructed the phylogenetic relationships between a batch of representative Neisseria meningitidis genomes. CC198 and CC1136 clustered together, but apart from other N. meningitidis strains including CC53. We also aligned the sequences of genes located in regions D and E of the capsule gene locus from encapsulated and unencapsulated strains. A number of possible recombination events were identified in the galE and tex genes between different serogroups of encapsulated N. meningitidis and CC53 strains, especially in tex. In contrast, there is almost no recombination in N. meningitidis CC198 strains. These results showed that CC198 belongs to a phylogenetically distinct group within the species N. meningitidis, which may be directly derived from the cnl-type ancestor of N. meningitidis. The encapsulated strains may acquire other necessary genes for capsule formation by horizontal transfer.

Kähler currents and null loci

We prove that the non-Kahler locus of a nef and big class on a compact complex manifold bimeromorphic to a Kahler manifold equals its null locus. In particular this gives an analytic proof of a theorem of Nakamaye and Ein-Lazarsfeld-Mustata-Nakamaye-Popa. As an application, we show that finite time non-collapsing singularities of the Kahler-Ricci flow on compact Kahler manifolds always form along analytic subvarieties, thus answering a question of Feldman-Ilmanen-Knopf and Campana. We also extend the second author's results about noncollapsing degenerations of Ricci-flat Kahler metrics on Calabi-Yau manifolds to the nonalgebraic case.

Genome Sequence of a Neisseria meningitidis Capsule Null Locus Strain from the Clonal Complex of Sequence Type 198

Neisseria meningitidis is a commensal and accidental pathogen exclusively of humans. Although the production of polysaccharide capsules is considered to be essential for meningococcal virulence, there have been reports of constitutively unencapsulated strains causing invasive meningococcal disease (IMD). Here we report the genome sequence of a capsule null locus (cnl) strain of sequence type 198 (ST-198), which is found in half of the reported cases of IMD caused by cnl meningococcal strains.

Capsule null locus meningococci: Typing of antigens used in an investigational multicomponent meningococcus serogroup B vaccine

The investigational multicomponent meningococcus serogroup B vaccine (4CMenB) targets the antigenetically variable population of serogroup B meningococci. Forty-one strains of capsule null locus (cnl) meningococci, which are frequent among healthy carriers, were selected from nine sequence types (ST), which belong to four clonal complexes (cc), and three countries. They were antigen sequence typed and analyzed for antigen expression to predict whether these strains harbor the genes and express the four vaccine antigens of 4CMenB as measured by the meningococcal antigen typing system (MATS). The PorA variant used in the vaccine was not found. The nadA gene was absent in all but one strain, which did not express the antigen in vitro. Only strains of clonal complex ST-198 harbored a factor H binding protein (FHBP) allele of the cross-reactive variant 1 family which is included in the vaccine. All these strains expressed the antigen. Five variants of the Neisserial heparin binding antigen (NHBA) gene were identified. Expression of NHBA was observed in all strains with highest levels in ST-198 cc and ST-845. The data suggest a potential impact of 4CMenB immunization at least on cnl meningococci of the ST-198 cc and ST-845.

Neisseria meningitidisStrain of Unknown Serogroup, China

<i>Neisseria meningitidis</i>Strain of Unknown Serogroup, China

Puroindolines co-localize to the starch granule surface and increase seed bound polar lipid content

Endosperm texture in wheat is controlled by the Pina and Pinb genes that comprise the Hardness ( Ha) locus. Studies have shown that soft and hard varieties differ in the amount of starch bound polar lipids but have not addressed whether PINs are directly involved and whether the presence of one particular PIN affects seed polar lipid levels and cellular localization. Here, we determined the effect of overexpressing PINA or PINB on seed bound polar lipids and PIN localization. F 3 recombinants homozygous for either a Pina or Pinb null Ha locus with or lacking a transgenically added Pina or Pinb were analyzed for grain hardness, PIN abundance, and seed bound polar lipid levels. Overexpressed PINs resulted in reduced hardness, increased starch bound PINs, and increased seed bound polar lipids. Addition of PINA to the PINA nulls or PINB to the PINB nulls resulted in higher bound polar lipid levels than the addition of the alternative PIN. Both PINs localized to the starch surface in the presence or absence of the other protein. Our results indicate that PIN overexpression results in reduced endosperm texture and increased seed bound polar lipids and that PINs independently localize to the surface of starch granules.

Three Cases of Invasive Meningococcal Disease Caused by a Capsule Null Locus Strain Circulating among Healthy Carriers in Burkina Faso

During reinforced surveillance of acute bacterial meningitis in Burkina Faso, meningococcal strains of phenotype NG:NT:NST were isolated from cerebrospinal fluid samples from 3 patients. The strains were negative for the ctrA gene but were positive for the crgA gene. Molecular typing revealed that the strains harbored the capsule null locus (cnl) and belonged to the multilocus sequence type (ST)-192. PorA sequencing showed that all strains were either P1.18-11,42; P1.18,42-1; P1.18-11,42-1; P1.18-11,42-3; or P1.18-12,42-1. Sequencing also showed that all strains were negative for the FetA receptor gene. Serum killing assays showed these strains to be resistant, with the resistance comparable with that of a fully capsular serogroup B strain, MC58. The same strains were found in 14 healthy carriers in the general population of Bobo-Dioulasso (100% of ST-192 isolates tested for cnl). The presence of cnl meningococci that can escape serum killing and cause invasive disease is of concern for future vaccination strategies and should promote rigorous surveillance of cnl meningococcal disease.

The Role of Puroindoline A and B Individually and in Combination on Grain Hardness and Starch Association

ABSTRACTEndosperm texture in wheat (Triticum aestivum L.) is an important criterion affecting end‐product quality. Grain hardness is controlled by the Hardness (Ha) locus which contains the puroindoline a (Pina) and puroindoline b (Pinb) genes. Hard wheats possess mutations in Pina or Pinb while soft wheats possess the Pina‐D1a and Pinb‐D1a alleles. Here, we determined the role of PINA and PINB individually and in combination on grain hardness and association to starch. Pina‐D1a or Pinb‐D1a overexpressing transgenic lines were crossed to PINA or PINB null hard wheats. The crosses segregated for the transgene and the Ha locus. Random lines from each genotypic class were evaluated in replicated trials over 2 yr. Classes containing only native levels of PINA or PINB were hard textured. Homozygous classes with transgenic addition of PINA to the PINA+/PINB null Ha locus or addition of PINB to the PINA+/PINB null Ha locus were intermediate in texture with grain hardness values of 43.5 and 45.5, respectively. Soft endosperm texture was only obtained when both PINA and PINB were present with the softest grain observed with addition of PINB to the PINA+/PINB null Ha locus. Association of high amounts of either puroindoline to starch required both PINA and PINB. The results indicate that PINA or PINB can act alone leading to intermediate‐textured grain or can function together to give a soft grain texture.

Rapid and Fatal Meningococcal Disease Due to a Strain of Neisseria meningitidis Containing the Capsule Null Locus

Neisseria meningitidis continues to be an important cause of invasive bacterial disease among children and young adults worldwide. In Canada, N. meningitidis strains that bear serogroups B and C polysaccharide capsules predominate. We report the first documented case of invasive meningococcal disease in an immunocompetent host caused by an acapsular strain of N. meningitidis containing the capsule null locus (cnl). Analysis of the isolate was performed with use of serological and molecular methods, including multilocus sequence typing and cnl gene identification. Analysis of 16S ribosomal RNA (rRNA) and porA genes was also performed to confirm the identity of the bacterium. The patient was a healthy, immunocompetent 13-year-old child, and N. meningitidis was recovered from a sample of her cerebrospinal fluid before death. The isolate was nontypeable by both conventional antisera and indirect whole-cell enzyme-linked immuosorbent assay methods using antibodies to serogroups B, C, Y, and W135. The isolate was further identified as a cnl strain, serotype 15 (ST-198). N. meningitidis-specific DNA was identified in the isolate and in the pre- and postmortem specimens by 16S rRNA and porA gene analysis. This is the first reported case of fatal meningococcal disease caused by an acapsular cnl strain of N. meningitidis that was isolated from an immunocompetent host. Routine molecular diagnostic methods targeted at the cnl locus failed to detect this organism, indicating a need to determine the incidence of infection with cnl strains among patients with culture-negative invasive disease.

Genes coding for starch branching enzymes are major contributors to starch viscosity characteristics in waxy rice (Oryza sativa L.)

Granule-bound starch synthase (GBSS) encoded by the Waxy (Wx) gene determines the synthesis of amylose; while, starch branching enzymes encoded by Sbe genes are involved in the formation of amylopectin. Both amylose and amylopectin form starch in the endosperm of seeds. Here, we report on the effects of the wx gene and the two Sbe genes, Sbe1 and Sbe3, on starch paste viscosity in waxy rice. Molecular markers for both Sbe1 and Sbe3 have been developed based on sequence diversity between the rice subspecies indica and japonica. All Sbe- and Wx- linked markers have been used to investigate 40 waxy rice cultivars. For the wx locus (null Wx locus in waxy rice), four classes of (CT)n repeats, including (CT)16, (CT)17, (CT)18, and (CT)19, were detected in the putative leader sequence. Moreover, a unique sequence, AGTTATA, is also present at the 5′ splice junction site of the putative leader intron. Overall, the wx locus has no effect on starch paste viscosity characteristics. Among all 40 waxy rice cultivars, five genotypes are observed at the Sbe1 and Sbe3 loci. Polymorphisms in both Sbe1 and Sbe3 loci account for ∼70% of the observed variations in both hot and cool viscosities, and for 40% of the observed variations in both peak viscosity and consistency.