Retrospective study using biosensor data of a milking Holstein cow with jejunal haemorrhage syndrome.

Jejunal haemorrhage syndrome (JHS) is a sporadic and fatal enterotoxaemic disease in dairy cows associated with acute development and poor prognosis despite treatment. A 5-year-old Holstein cow with no reported pregnancy, three calving numbers, and 303 days in milk presented with hypothermia, discomfort, and inappetence. Anaemia, dehydration, faeces with blood clots, and absence of rumen and bowel movements were observed. We identified the presence of neutrophilia, hyperglycaemia, hypoproteinaemia, azotaemia, hyperlactatemia, hypocalcaemia, hypermagnesemia, hypokalaemia, and hypochloraemia through blood analyses. Necropsy and histopathologic examination revealed a dilated bluish-purple jejunum, blood clots within the jejunum, neutrophil infiltration into the submucosa of the jejunum, and vascular necrosis. Retrospective examination revealed extraordinary patterns of rumination time, activity, rumen mobility, and rumen temperature using biosensors and decreased milk yield. The abnormalities in the affected cow were detected before recognition by farm workers. To the best of our knowledge, this is the first report to examine data from biosensors in a cow with JHS. Our findings suggest that using biometric data may help understand the development of JHS.

A Novel Synthetic Antibody Library with Complementarity-Determining Region Diversities Designed for an Improved Amplification Profile.

Antibody discovery by phage display consists of two phases, i.e., the binding phase and the amplification phase. Ideally, the selection process is dominated by the former, and all the retrieved clones are amplified equally during the latter. In reality, the amplification efficiency of antibody fragments varies widely among different sequences and, after a few rounds of phage display panning, the output repertoire often includes rapidly amplified sequences with low or no binding activity, significantly diminishing the efficiency of antibody isolation. In this work, a novel synthetic single-chain variable fragment (scFv) library with complementarity-determining region (CDR) diversities aimed at improved amplification efficiency was designed and constructed. A previously reported synthetic scFv library with low, non-combinatorial CDR diversities was panned against protein A superantigen, and the library repertoires before and after the panning were analyzed by next generation sequencing. The enrichment or depletion patterns of CDR sequences after panning served as the basis for the design of the new library. Especially for CDR-H3 with a higher and more random diversity, a machine learning method was applied to predict potential fast-amplified sequences among a simulated sequence repertoire. In a direct comparison with the previous generation library, the new library performed better against a panel of antigens in terms of the number of binders isolated, the number of unique sequences, and/or the speed of binder enrichment. Our results suggest that the amplification-centric design of sequence diversity is a valid strategy for the construction of highly functional phage display antibody libraries.

Metabolic engineering of Klebsiella pneumoniae for the production of cis,cis-muconic acid.

cis,cis-Muconic acid (ccMA), a metabolic intermediate of Klebsiella pneumoniae, can be converted to adipic acid and terephthalic acid, which are important monomers of synthetic polymers. However, wild-type K. pneumoniae does not produce ccMA because intracellular carbon flow does not favor ccMA biosynthesis. In this study, several metabolic engineering strategies were used in an attempt to modify the wild-type strain to induce it to produce ccMA. First, by blocking the synthesis of aromatic amino acids, 343 mg/L of catechol, a precursor of ccMA, was produced. Then, the native catechol 1,2-dioxygenasegene (catA) was overexpressed, which caused the strain to convert the catechol to ccMA. The production of ccMA was further improved by deletion of the muconate cycloisomerase gene (catB) and by deleting a feedback inhibitor of the aromatic amino acid pathway. Further improvement was achieved by adjusting the pH of the culture broth. The developed strain produced 2.1 g/L of ccMA in flask cultivation. The results showed the potential of K. pneumoniae as a ccMA producer.

Improvement of 2,3-butanediol yield in Klebsiella pneumoniae by deletion of the pyruvate formate-lyase gene.

Klebsiella pneumoniae is considered a good host strain for the production of 2,3-butanediol, which is a promising platform chemical with various industrial applications. In this study, three genes, including those encoding glucosyltransferase (wabG), lactate dehydrogenase (ldhA), and pyruvate formate-lyase (pflB), were disrupted in K. pneumoniae to reduce both its pathogenic characteristics and the production of several by-products. In flask cultivation with minimal medium, the yield of 2,3-butanediol from rationally engineered K. pneumoniae (ΔwabG ΔldhA ΔpflB) reached 0.461 g/g glucose, which was 92.2% of the theoretical maximum, with a significant reduction in by-product formation. However, the growth rate of the pflB mutant was slightly reduced compared to that of its parental strain. Comparison with similar mutants of Escherichia coli suggested that the growth defect of pflB-deficient K. pneumoniae was caused by redox imbalance rather than reduced level of intracellular acetyl coenzyme A (acetyl-CoA). From an analysis of the transcriptome, it was confirmed that the removal of pflB from K. pneumoniae significantly repressed the expression of genes involved in the formate hydrogen lyase (FHL) system.

A single-domain antibody library based on a stability-engineered human VH3 scaffold.

Using conventional immunoglobulin G (IgG) molecules as therapeutic agents presents several well-known disadvantages owing to their large size and structural complexity, negatively impacting development and production efficiency. Single-domain antibodies (sdAbs) are the smallest functional antibody format (~ 15 kDa) and represent a viable alternative to IgG in many applications. However, unlike natural single-domain antibodies, such as camelid VHH, the variable domains of conventional antibodies show poor physicochemical properties when expressed as sdAbs. This report identified stable sdAb variants of human VH3-23 from a framework region 2-randomized human VH library by phage display selection under thermal challenge. Synthetic complementarity determining region diversity was introduced to one of the selected variants with high thermal stability, expression level, and monomeric content to construct a human VH sdAb library. The library was validated by panning against a panel of antigens, and target-specific binders were identified and characterized for their affinity and biophysical properties. The results of this study suggest that a synthetic sdAb library based on a stability-engineered human VH scaffold could be a facile source of high-quality sdAb for many practical applications.

Effects of subclinical mastitis on automatic milking system data, hematological and biochemical parameters, and milk composition in Holstein cows.

Objective: Subclinical mastitis decreases milk production and quality, despite the normal appearance of the mammary glands and milk. Herein, we aimed to investigate changes in factors monitored via automatic milking systems (AMS) prior to subclinical mastitis onset and identify differences in hematological and biochemical parameters and milk composition at subclinical mastitis onset. Methods: Thirty-two Holstein cows were divided into two groups according to somatic cell counts (SCC) from AMS and milk composition analysis and the California mastitis test (CMT): healthy cows (controls [CON], n=16, SCC <500×103 cells/ml and negative for CMT) and cows with subclinical mastitis (SCM, n=16, SCC ≥500×103 cells/ml and positive for CMT). Eventually, 121 milk samples from the CON ([mCON], n=60) and SCM ([mSCM], n=61) groups were obtained; SCM samples were categorized as those from non-inflamed (mNQ) or subclinically-inflamed (mIQ) quarters. We evaluated AMS factors; hematological, biochemical, and milk composition parameters; and bacterial isolation. Results: In cows with SCM, milk yield decreased and electrical conductivity (EC) changed before disease onset. Milk EC decreased in mNQ although increased in mIQ (p<0.05). The SCM group had higher globulin levels and lower basophil counts; albumin-to-globulin ratio; and total cholesterol, albumin, and blood urea nitrogen levels than the CON group (p<0.05). The mIQ group had higher SCC but lower levels of lactose and milk solids-not-fat than those in the mCON and mNQ groups (p<0.05). The mCON group had higher levels of milk non-protein nitrogen than the mNQ group (p<0.05). Opportunistic mastitis pathogens were isolated in the mIQ group. Conclusion: Changes in milk yield and EC measured using AMS occurred prior to subclinical mastitis, which may be associated with variation in basophil counts; albumin-to-globulin ratio; and total cholesterol, albumin, BUN, globulin, SCC, milk lactose, and milk solids-not-fat levels at disease onset. These findings provide new insights into early-stage subclinical mastitis.

Butyrate production in engineered Escherichia coli with synthetic scaffolds.

Butyrate pathway was constructed in recombinant Escherichia coli using the genes from Clostridium acetobutylicum and Treponema denticola. However, the pathway constructed from exogenous enzymes did not efficiently convert carbon flux to butyrate. Three steps of the productivity enhancement were attempted in this study. First, pathway engineering to delete metabolic pathways to by-products successfully improved the butyrate production. Second, synthetic scaffold protein that spatially co-localizes enzymes was introduced to improve the efficiency of the heterologous pathway enzymes, resulting in threefold improvement in butyrate production. Finally, further optimizations of inducer concentrations and pH adjustment were tried. The final titer of butyrate was 4.3 and 7.2 g/L under batch and fed-batch cultivation, respectively. This study demonstrated the importance of synthetic scaffold protein as a useful tool for optimization of heterologous butyrate pathway in E. coli.

Comparison of blood parameters according to fecal detection of Mycobacterium avium subspecies paratuberculosis in subclinically infected Holstein cattle.

BACKGROUND: Mycobacterium avium subspecies paratuberculosis (MAP) causes a chronic and progressive granulomatous enteritis and economic losses in dairy cattle in subclinical stages. Subclinical infection in cattle can be detected using serum MAP antibody enzyme-linked immunosorbent assay (ELISA) and fecal polymerase chain reaction (PCR) tests. OBJECTIVES: To investigate the differences in blood parameters, according to the detection of MAP using serum antibody ELISA and fecal PCR tests. METHODS: We divided 33 subclinically infected adult cattle into three groups: seronegative and fecal-positive (SNFP, n = 5), seropositive and fecal-negative (SPFN, n = 10), and seropositive and fecal-positive (SPFP, n = 18). Hematological and serum biochemical analyses were performed. RESULTS: Although the cows were clinically healthy without any manifestations, the SNFP and SPFP groups had higher platelet counts, mean platelet volumes, plateletcrit, lactate dehydrogenase levels, lactate levels, and calcium levels but lower mean corpuscular volume concentration than the SPFN group (p < 0.017). The red blood cell count, hematocrit, monocyte count, glucose level, and calprotectin level were different according to the detection method (p < 0.05). The SNFP and SPFP groups had higher red blood cell counts, hematocrit and calprotectin levels, but lower monocyte counts and glucose levels than the SPFN group, although there were no significant differences (p > 0.017). CONCLUSIONS: The cows with fecal-positive MAP status had different blood parameters from those with fecal-negative MAP status, although they were subclinically infected. These findings provide new insights into understanding the mechanism of MAP infection in subclinically infected cattle.

Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering.

BACKGROUND: 2,3-Butanediol is a chemical compound of increasing interest due to its wide applications. It can be synthesized via mixed acid fermentation of pathogenic bacteria such as Enterobacter aerogenes and Klebsiella oxytoca. The non-pathogenic Saccharomyces cerevisiae possesses three different 2,3-butanediol biosynthetic pathways, but produces minute amount of 2,3-butanediol. Hence, we attempted to engineer S. cerevisiae strain to enhance 2,3-butanediol production. RESULTS: We first identified gene deletion strategy by performing in silico genome-scale metabolic analysis. Based on the best in silico strategy, in which disruption of alcohol dehydrogenase (ADH) pathway is required, we then constructed gene deletion mutant strains and performed batch cultivation of the strains. Deletion of three ADH genes, ADH1, ADH3 and ADH5, increased 2,3-butanediol production by 55-fold under microaerobic condition. However, overproduction of glycerol was observed in this triple deletion strain. Additional rational design to reduce glycerol production by GPD2 deletion altered the carbon fluxes back to ethanol and significantly reduced 2,3-butanediol production. Deletion of ALD6 reduced acetate production in strains lacking major ADH isozymes, but it did not favor 2,3-butanediol production. Finally, we introduced 2,3-butanediol biosynthetic pathway from Bacillus subtilis and E. aerogenes to the engineered strain and successfully increased titer and yield. Highest 2,3-butanediol titer (2.29 . l-1) and yield (0.113 g . g-1) were achieved by Δadh1 Δadh3 Δadh5 strain under anaerobic condition. CONCLUSIONS: With the aid of in silico metabolic engineering, we have successfully designed and constructed S. cerevisiae strains with improved 2,3-butanediol production.

Deletion of lactate dehydrogenase in Enterobacter aerogenes to enhance 2,3-butanediol production.

2,3-Butanediol is an important bio-based chemical product, because it can be converted into several C4 industrial chemicals. In this study, a lactate dehydrogenase-deleted mutant was constructed to improve 2,3-butanediol productivity in Enterobacter aerogenes. To delete the gene encoding lactate dehydrogenase, λ Red recombination method was successfully adapted for E. aerogenes. The resulting strain produced a very small amount of lactate and 16.7% more 2,3-butanediol than that of the wild-type strain in batch fermentation. The mutant and its parental strain were then cultured with six different carbon sources, and the mutant showed higher carbon source consumption and microbial growth rates in all media. The 2,3-butanediol titer reached 69.5 g/l in 54 h during fed-batch fermentation with the mutant,which was 27.4% higher than that with the parental strain.With further optimization of the medium and aeration conditions,118.05 g/l 2,3-butanediol was produced in 54 h during fed-batch fermentation with the mutant. This is by far the highest titer of 2,3-butanediol with E. aerogenes achieved by metabolic pathway engineering.

An in vitro study of the antifungal effect of silver nanoparticles on oak wilt pathogen Raffaelea sp.

In this study, we investigated the antifungal activity of three different forms of silver nanoparticles against the unidentified ambrosia fungus Raffaelea sp., which has been responsible for the mortality of a large number of oak trees in Korea. Growth of fungi in the presence of silver nanoparticles was significantly inhibited in a dosedependent manner. We also assessed the effectiveness of combining the different forms of nanoparticles. Microscopic observation revealed that silver nanoparticles caused detrimental effects not only on fungal hyphae but also on conidial germination.

High-yield production of 1,3-propanediol from glycerol by metabolically engineered Klebsiella pneumoniae.

BACKGROUND: Glycerol is a major byproduct of the biodiesel industry and can be converted to 1,3-propanediol (1,3-PDO) by microorganisms through a two-step enzymatic reaction. The production of 1,3-PDO from glycerol using microorganisms is accompanied by formation of unwanted byproducts, including lactate and 2,3-butanediol, resulting in a low-conversion yield. RESULTS: Klebsiella pneumoniae was metabolically engineered to produce high-molar yield of 1,3-PDO from glycerol. First, the pathway genes for byproduct formation were deleted in K. pneumoniae. Then, glycerol assimilation pathways were eliminated and mannitol was co-fed to the medium. Finally, transcriptional regulation of the dha operon were genetically modified for enhancing 1,3-propanediol production. The batch fermentation of the engineered strain with co-feeding of a small amount of mannitol yielded 0.76 mol 1,3-PDO from 1 mol glycerol. CONCLUSIONS: Klebsiella pneumoniae is useful microorganism for producing 1,3-PDO from glycerol. Implemented engineering in this study successfully improved 1,3-PDO production yield, which is significantly higher than those reported in previous studies.

Pathway engineering of Enterobacter aerogenes to improve acetoin production by reducing by-products formation.

Enterobacter aerogenes was metabolically engineered for acetoin production. To remove the pathway enzymes that catalyzed the formation of by-products, the three genes encoding a lactate dehydrogenase (ldhA) and two 2,3-butanediol dehydrogenases (budC, and dhaD), respectively, were deleted from the genome. The acetoin production was higher under highly aerobic conditions. However, an extracellular glucose oxidative pathway in E. aerogenes was activated under the aerobic conditions, resulting in the accumulation of 2-ketogluconate. To decrease the accumulation of this by-product, the gene encoding a glucose dehydrogenase (gcd) was also deleted. The resulting strain did not produce 2-ketogluconate but produced significant amounts of acetoin, with concentration reaching 71.7g/L with 2.87g/L/h productivity in fed-batch fermentation. This result demonstrated the importance of blocking the glucose oxidative pathway under highly aerobic conditions for acetoin production using E. aerogenes.

Metabolic engineering of Enterobacter aerogenes for 2,3-butanediol production from sugarcane bagasse hydrolysate.

The pathway engineering of Enterobacter aerogenes was attempted to improve its production capability of 2,3-butanediol from lignocellulosic biomass. In the medium containing glucose and xylose mixture as carbon sources, the gene deletion of pflB improved 2,3-butanediol carbon yield by 40%, while the deletion of ptsG increased xylose consumption rate significantly, improving the productivity at 12 hr by 70%. The constructed strain, EMY-22-galP, overexpressing glucose transporter (galP) in the triple gene knockout E. aerogenes, ldhA, pflB, and ptsG, provided the highest 2,3-butanediol titer and yield at 12 hr flask cultivation. Sugarcane bagasse was pretreated with green liquor, a solution containing Na2CO3 and Na2SO3 and was hydrolyzed by enzymes. The resulting hydrolysate was used as a carbon source for 2,3-butanediol production. After 72 hr in fermentation, the yield of 0.395g/g sugar was achieved, suggesting an economic production of 2,3-butanediol was possible from lignocellulosic biomass with the metabolically engineered strain.

Reutilization of green liquor chemicals for pretreatment of whole rice waste biomass and its application to 2,3-butanediol production.

The performance of green liquor pretreatment using Na2CO3 and Na2SO3 and its optimization for whole rice waste biomass (RWB) was investigated. Incubation of Na2CO3-Na2SO3 at a 1:1 ratio (chemical charge 10%) for 12% RWB at 100°C for 6h resulted in maximum delignification (58.2%) with significant glucan yield (88%) and total sugar recovery (545mg/g of RWB) after enzymatic hydrolysis. Recovery and reusability of the resulting chemical spent wash were evaluated to treat RWB along with its compatibility for enzymatic digestibility. Significant hydrolysis and lignin removal were observed for up to three cycles; however, further reuse of Na2CO3 and Na2SO3 lowered their performance. Significant 2,3-butanediol (BDO) was produced by Klebsiella pneumoniae KMK-05 with the RWB enzymatic hydrolysate from each pretreatment cycle. BDO yield achieved using RWB-derived sugars was similar to those using laboratory-grade sugars. This pretreatment strategy constitutes an ecofriendly, cost-effective, and practical method for utilizing lignocellulosic biomass.

Alleviation of carbon catabolite repression in Enterobacter aerogenes for efficient utilization of sugarcane molasses for 2,3-butanediol production.

BACKGROUND: Due to its cost-effectiveness and rich sugar composition, sugarcane molasses is considered to be a promising carbon source for biorefinery. However, the sugar mixture in sugarcane molasses is not consumed as efficiently as glucose in microbial fermentation due to complex interactions among their utilizing pathways, such as carbon catabolite repression (CCR). In this study, 2,3-butanediol-producing Enterobacter aerogenes was engineered to alleviate CCR and improve sugar utilization by modulating its carbon preference. RESULTS: The gene encoding catabolite repressor/activator (Cra) was deleted in the genome of E. aerogenes to increase the fructose consumption rate. However, the deletion mutation repressed sucrose utilization, resulting in the accumulation of sucrose in the fermentation medium. Cra regulation on expression of the scrAB operon involved in sucrose catabolism was verified by reverse transcription and real-time PCR, and the efficiency of sucrose utilization was restored by disrupting the scrR gene and overexpressing the scrAB operon. In addition, overexpression of the ptsG gene involved in glucose utilization enhanced the glucose preference among mixed sugars, which relieved glucose accumulation in fed-batch fermentation. In fed-batch fermentation using sugarcane molasses, the maximum titer of 2,3-butanediol production by the mutant reached 140.0 g/L at 54 h, which was by far the highest titer of 2,3-butanediol with E. aerogenes achieved through genetic engineering. CONCLUSIONS: We have developed genetically engineered E. aerogenes as a 2,3-butanediol producer that efficiently utilizes sugarcane molasses. The fermentation efficiency was dramatically improved by the alleviation of CCR and modulation of carbon preference. These results offer a metabolic engineering approach for achieving highly efficient utilization of mixed sugars for the biorefinery industry.

Engineered Enterobacter aerogenes for efficient utilization of sugarcane molasses in 2,3-butanediol production.

Sugarcane molasses is considered to be a good carbon source for biorefinery due to its high sugar content and low price. Sucrose occupies more than half of the sugar in the molasses. Enterobacter aerogenes is a good host strain for 2,3-butanediol production, but its utilization of sucrose is not very efficient. To improve sucrose utilization in E. aerogenes, a sucrose regulator (ScrR) was disrupted from the genomic DNA. The deletion mutation increased the sucrose consumption rate significantly when sucrose or sugarcane molasses was used as a carbon source. The 2,3-butanediol production from sugarcane molasses by the mutant was enhanced by 60% in batch fermentation compared to that by the wild type strain. In fed-batch fermentation, 98.69 g/L of 2,3-butanediol production was achieved at 36 h.

Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice.

We have generated 47,932 T-DNA tag lines in japonica rice using activation-tagging vectors that contain tetramerized 35S enhancer sequences. To facilitate use of those lines, we isolated the genomic sequences flanking the inserted T-DNA via inverse polymerase chain reaction. For most of the lines, we performed four sets of amplifications using two different restriction enzymes toward both directions. In analyzing 41,234 lines, we obtained 27,621 flanking sequence tags (FSTs), among which 12,505 were integrated into genic regions and 15,116 into intergenic regions. Mapping of the FSTs on chromosomes revealed that T-DNA integration frequency was generally proportional to chromosome size. However, T-DNA insertions were non-uniformly distributed on each chromosome: higher at the distal ends and lower in regions close to the centromeres. In addition, several regions showed extreme peaks and valleys of insertion frequency, suggesting hot and cold spots for T-DNA integration. The density of insertion events was somewhat correlated with expressed, rather than predicted, gene density along each chromosome. Analyses of expression patterns near the inserted enhancer showed that at least half the test lines displayed greater expression of the tagged genes. Whereas in most of the increased lines expression patterns after activation were similar to those in the wild type, thereby maintaining the endogenous patterns, the remaining lines showed changes in expression in the activation tagged lines. In this case, ectopic expression was most frequently observed in mature leaves. Currently, the database can be searched with the gene locus number or location on the chromosome at http://www.postech.ac.kr/life/pfg/risd. On request, seeds of the T(1) or T(2) plants will be provided to the scientific community.