Variations in antibody repertoires correlate with vaccine responses.

An important challenge in vaccine development is to figure out why a vaccine succeeds in some individuals and fails in others. Although antibody repertoires hold the key to answering this question, there have been very few personalized immunogenomics studies so far aimed at revealing how variations in immunoglobulin genes affect a vaccine response. We conducted an immunosequencing study of 204 calves vaccinated against bovine respiratory disease (BRD) with the goal to reveal variations in immunoglobulin genes and somatic hypermutations that impact the efficacy of vaccine response. Our study represents the largest longitudinal personalized immunogenomics study reported to date across all species, including humans. To analyze the generated data set, we developed an algorithm for identifying variations of the immunoglobulin genes (as well as frequent somatic hypermutations) that affect various features of the antibody repertoire and titers of neutralizing antibodies. In contrast to relatively short human antibodies, cattle have a large fraction of ultralong antibodies that have opened new therapeutic opportunities. Our study reveals that ultralong antibodies are a key component of the immune response against the costliest disease of beef cattle in North America. The detected variants of the cattle immunoglobulin genes, which are implicated in the success/failure of the BRD vaccine, have the potential to direct the selection of individual cattle for ongoing breeding programs.

metaFlye: scalable long-read metagenome assembly using repeat graphs.

Long-read sequencing technologies have substantially improved the assemblies of many isolate bacterial genomes as compared to fragmented short-read assemblies. However, assembling complex metagenomic datasets remains difficult even for state-of-the-art long-read assemblers. Here we present metaFlye, which addresses important long-read metagenomic assembly challenges, such as uneven bacterial composition and intra-species heterogeneity. First, we benchmarked metaFlye using simulated and mock bacterial communities and show that it consistently produces assemblies with better completeness and contiguity than state-of-the-art long-read assemblers. Second, we performed long-read sequencing of the sheep microbiome and applied metaFlye to reconstruct 63 complete or nearly complete bacterial genomes within single contigs. Finally, we show that long-read assembly of human microbiomes enables the discovery of full-length biosynthetic gene clusters that encode biomedically important natural products.

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.

Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.

Factors Associated With Upper Extremity Functional Recovery Following Low-Frequency Repetitive Transcranial Magnetic Stimulation in Stroke Patients.

OBJECTIVE: To investigate the factors related to upper extremity functional improvement following inhibitory repetitive transcranial magnetic stimulation (rTMS) in stroke patients. METHODS: Forty-one stroke patients received low-frequency rTMS over the contralesional hemisphere according to a standard protocol, in addition to conventional physical and occupational therapy. The rTMS-treated patients were divided into two groups according to their responsiveness to rTMS measured by the self-care score of the Korean version of Modified Barthel Index (K-MBI): responded group (n=19) and non-responded group (n=22). Forty-one age-matched stroke patients who had not received rTMS served as controls. Neurological, cognitive and functional assessments were performed before rTMS and 4 weeks after rTMS treatment. RESULTS: Among the rTMS-treated patients, the responded group was significantly younger than the non-responded group (51.6±10.5 years and 65.5±13.7 years, respectively; p=0.001). Four weeks after rTMS, the National Institutes of Health Stroke Scale, the Brunnstrom recovery stage and upper extremity muscle power scores were significantly more improved in the responded group than in the control group. Besides the self-care score, the mobility score of the K-MBI was also more improved in the responded group than in the non-responded group or controls. CONCLUSION: Age is the most obvious factor determining upper extremity functional responsiveness to low-frequency rTMS in stroke patients.

The Prediction of Clinical Outcome Using HbA1c in Acute Ischemic Stroke of the Deep Branch of Middle Cerebral Artery.

OBJECTIVE: To elucidate the association between glycemic control status and clinical outcomes in patients with acute ischemic stroke limited to the deep branch of the middle cerebral artery (MCA). METHODS: We evaluated 65 subjects with first-ever ischemic stroke of the deep branches of the MCA, which was confirmed by magnetic resonance angiography. All subjects had blood hemoglobin A1c (HbA1c) measured at admission. They were classified into two groups according to the level of HbA1c (low <7.0% or high ≥7.0%). Neurological impairment and functional status were evaluated using the National Institutes of Health Stroke Scale (NIHSS), Functional Independence Measure (FIM), Korean version of Modified Barthel Index (K-MBI), Korean version of Mini-Mental State Examination (MMSE-K), and the Loewenstein Occupational Therapy Cognitive Assessment (LOTCA) at admission and discharge. Body mass index, serum glucose, homocysteine and cholesterol levels were also measured at admission. RESULTS: The two groups did not show any difference in the NIHSS, FIM, K-MBI, MMSE-K, and LOTCA scores at any time point. Body mass index and levels of blood homocysteine and cholesterol were not different between the two groups. The serum blood glucose level at admission was negatively correlated with all outcome measures. CONCLUSION: We found that HbA1c cannot be used for predication of clinical outcome in patients with ischemic stroke of the deep branch of the middle cerebral artery.

A pollen-specific calmodulin-binding protein, NPG1, interacts with putative pectate lyases.

Previous genetic studies have revealed that a pollen-specific calmodulin-binding protein, No Pollen Germination 1 (NPG1), is required for pollen germination. However, its mode of action is unknown. Here we report direct interaction of NPG1 with pectate lyase-like proteins (PLLs). A truncated form of AtNPG1 lacking the N-terminal tetratricopeptide repeat 1 (TPR1) failed to interact with PLLs, suggesting that it is essential for NPG1 interaction with PLLs. Localization studies with AtNPG1 fused to a fluorescent reporter driven by its native promoter revealed its presence in the cytosol and cell wall of the pollen grain and the growing pollen tube of plasmolyzed pollen. Together, our data suggest that the function of NPG1 in regulating pollen germination is mediated through its interaction with PLLs, which may modify the pollen cell wall and regulate pollen tube emergence and growth.

Organ-specific, developmental, hormonal and stress regulation of expression of putative pectate lyase genes in Arabidopsis.

Pectate lyases catalyse the eliminative cleavage of de-esterified homogalacturonan in pectin, a major component of the primary cell walls in higher plants. In the completed genome of Arabidopsis, there are 26 genes (AtPLLs) that encode pectate lyase-like proteins. Here, we analysed the expression pattern of all AtPLLs in different organs, at different stages of seedling development and in response to various hormones and stresses. The expression of PLLs varied considerably in different organs, with no expression of some PLLs in vegetative organs. Interestingly, all PLL genes are expressed in flowers. Several PLLs are expressed highly in pollen, suggesting a role for these in pollen development and/or function. Analysis of expression of all PLL genes in seedlings treated with hormones, abiotic stresses and elicitors of defense responses revealed significant changes in the expression of some PLLs without affecting the other PLLs. The stability of transcripts of PLLs varied considerably among different genes. Our results indicate a complex regulation of expression of PLLs and involvement of PLLs in some of the hormonal and stress responses.