Comparative analysis of thermal indices for modeling cold and heat stress in US dairy systems.

Quantifying the impact of thermal stress on milk yields is essential to effectively manage present and future risks in dairy systems. Despite the existence of numerous heat indices designed to communicate stress thresholds, little information is available regarding the accuracy of different indices in estimating milk yield losses from both cold and heat stress at large spatio-temporal scales. To address this gap, we comparatively analyzed the performance of existing thermal indices in capturing US milk yield response to both cold and heat stress at the national scale. We selected four commonly used thermal indices: the Temperature and Humidity Index (THI), Black Globe Humidity Index (BGHI), Adjusted Temperature and Humidity Index (THIadj), and Comprehensive Climate Index (CCI). Using a statistical panel regression model with observational and reanalysis weather data from 1981-2020, we systematically compared the patterns of yield sensitivities and statistical performance of the four indices. We found that the US state-level milk yield variability was better explained by the THIadj and CCI, which combine the effects of temperature, humidity, wind, and solar radiation. Our analysis also reveals a continuous and nonlinear responses of milk yields to a range of cold to heat stress across all four indices. This implies that solely relying on fixed thresholds of these indices to model milk yield changes may be insufficient to capture cumulative thermal stress. Cold extremes reduced milk yields comparably to those impacted by heat extremes on the national scale. Additionally, we found large spatial variability in milk yield sensitivities, implying further limitations to the use of fixed thresholds across locations. Moreover, we found decreased yield sensitivity to thermal stress in the most recent two decades, suggesting adaptive changes in management to reduce weather-related risks.

Economic and environmental effects of double cropping winter annuals and corn using the Integrated Farm System Model.

Dairy farms have been under pressure to reduce negative environmental impacts while remaining profitable during times with volatile milk and commodity prices. Double cropping has been promoted to reduce negative environmental impacts and increase total dry matter yield per hectare. Three dairy farms that double cropped winter annuals and corn were selected from northern and western Pennsylvania. Data were collected from recorded crop and dairy records and financial data for 2016 and 2017. Farms ranged in size from 336 to 511 ha with 233 to 663 cows. Data were used to set parameters for the Integrated Farm System Model, which was then used to simulate 8 scenarios for each farm: current operation; 0, 50, and 100% of corn hectares double cropped; 30% feed price increase with and without double cropping; and 30% feed price decrease with and without double cropping at the farm's current level of double cropping. A 20-yr time period, using weather data that was representative of the actual farms, was used in the Integrated Farm System Model simulation to produce both financial and environmental outputs. Double cropping winter annuals and corn silage increased dry matter yield per hectare by 19%, when comparing 0 to 100% of the corn area double cropped. With all corn land double cropped, net return to management per hundredweight (45.36 kg) of milk increased by 1.8%, N leached per hectare per year decreased by an average of 4.5%, and phosphorus loss was reduced by an average of 9.2% across farms. When feed prices increased by 30%, double cropping increased net return over feed cost and net return to management by 1.6 and 2.2%, respectively, across farms. When feed prices decreased by 30%, double cropping decreased net return over feed cost and net return to management by smaller amounts of 0.13% and 0.11%, respectively, across farms. Modeling indicated that double cropping winter annuals with corn silage can have both environmental and economic benefits when winter-annual silage yields are enough to cover expenses.

Genetic effects on birth weight in reciprocal Brahman-Simmental crossbred calves.

Brahman-cross calves exhibit unusual inheritance of birth weight: Brahman-sired crossbreds out of females are heavier with greater difference between sexes than calves of the reciprocal cross. The objectives of this work were to confirm that unusual inheritance and to investigate non-Mendelian genetic effects that may influence differences in Brahman × Simmental crossbred calves. Crossbred calves were produced by embryo transfer ( = 2,862) and natural service or artificial insemination ( = 2,125) from 1983 to 1991 by a private seedstock producer. Brahman-sired F embryos out of Simmental donors weighed 9.4 ± 1.1 ( < 0.001) kg more at birth than Simmental-sired F embryos out of Brahman donor cows when transferred to comparable recipients. This reciprocal difference was accompanied by sexual dimorphism: within Brahman-sired F calves, males were 5.0 ± 1.4 kg heavier than females, whereas within Simmental-sired F calves, females were 0.7 ± 0.5 kg heavier than males. Covariates were constructed from the pedigree to represent genetic effects: proportion Brahman in calves and dams (direct and maternal breed effects), direct and maternal breed heterozygosity, probability of Brahman mitochondrial origin, probability of Brahman Y chromosome, probability of Brahman X chromosome, genomic imprinting (the difference between the probabilities of Brahman in the genetic dam and in the sire), nonrandom X inactivation by breed of origin (the probability of breed heterozygosity of the X chromosomes of a female), and nonrandom X inactivation by parent of origin (the difference between probabilities of a female inheriting a paternal or maternal Brahman X chromosome). The maternal breed heterozygosity, genomic imprinting, probability of Brahman X chromosome, and genomic imprinting × sex effect covariates from the full model were significant with regression coefficients of 1.1 ± 0.5 ( < 0.05), ‒8.3 ± 2.3 ( < 0.01), ‒3.5 ± 1.3 ( < 0.01), and ‒5.3 ± 2.0 ( < 0.01), respectively. Results suggest that sex-specific genomic imprinting may be contributing to the inheritance of birth weight in crossbred calves, similar to patterns of mouse litter and placental weight in interspecific crosses.

Integration host factor interactions with Neisseria gene sequences: correlation between predicted binding sites and in vitro binding of Neisseria -derived IHF protein.

Putative integration host factor (IHF) binding sites are frequently being identified in Neisseria gene sequences on the basis of similarity to a degenerate Escherichia coli -derived consensus binding sequence. In this report, three different Neisseria genetic systems that contain predicted IHF binding sites were assessed for IHF binding through gel retardation analysis. The results show a positive correlation between the identification of a predicted Neisseria IHF binding site and in vitro binding of Neisseria -derived IHF protein.

Gonococcal MinD affects cell division in Neisseria gonorrhoeae and Escherichia coli and exhibits a novel self-interaction.

The Min proteins are involved in determining cell division sites in bacteria and have been studied extensively in rod-shaped bacteria. We have recently shown that the gram-negative coccus Neisseria gonorrhoeae contains a min operon, and the present study investigates the role of minD from this operon. A gonococcal minD insertional mutant, CJSD1, was constructed and exhibited both grossly abnormal cell division and morphology as well as altered cell viability. Western blot analysis verified the absence of MinD from N. gonorrhoeae (MinD(Ng)) in this mutant. Hence, MinD(Ng) is required for maintaining proper cell division and growth in N. gonorrhoeae. Immunoblotting of soluble and insoluble gonococcal cell fractions revealed that MinD(Ng) is both cytosolic and associated with the insoluble membrane fraction. The joint overexpression of MinC(Ng) and MinD(Ng) from a shuttle vector resulted in a significant enlargement of gonococcal cells, while cells transformed with plasmids encoding either MinC(Ng) or MinD(Ng) alone did not display noticeable morphological changes. These studies suggest that MinD(Ng) is involved in inhibiting gonococcal cell division, likely in conjunction with MinC(Ng). The alignment of MinD sequences from various bacteria showed that the proteins are highly conserved and share several regions of identity, including a conserved ATP-binding cassette. The overexpression of MinD(Ng) in wild-type Escherichia coli led to cell filamentation, while overexpression in an E. coli minD mutant restored a wild-type morphology to the majority of cells; therefore, gonococcal MinD is functional across species. Yeast two-hybrid studies and gel-filtration and sedimentation equilibrium analyses of purified His-tagged MinD(Ng) revealed a novel MinD(Ng) self-interaction. We have also shown by yeast two-hybrid analysis that MinD from E. coli interacts with itself and with MinD(Ng). These results indicate that MinD(Ng) is required for maintaining proper cell division and growth in N. gonorrhoeae and suggests that the self-interaction of MinD may be important for cell division site selection across species.

Multiple origins and replication proteins influence biological properties of beta-lactamase-producing plasmids from Neisseria gonorrhoeae.

The beta-lactamase-producing Asia-type plasmid pJD4 of Neisseria gonorrhoeae is a 7.4-kb, broad-host-range plasmid. It is part of a family of plasmids which are structurally related yet vary in size, found in both N. gonorrhoeae and Haemophilus ducreyi. Branch-point analysis by electron microscopy indicates that pJD4 carries three clustered but distinguishable origins of replication, which we named ori1, ori2, and ori3. Although pJD4 belongs to incompatibility (Inc) group W, it also carries a silent IncFII determinant which is expressed when ori2 and ori3 are absent. The Africa-type plasmid pJD5, a naturally occurring deletion derivative of pJD4, carries only ori1, belongs to the IncFII group, and, in contrast to pJD4, requires DNA polymerase I (Pol I) for replication. Plasmids constructed from pJD4 which lack ori1 but carry ori2 and ori3 do not require Pol I and are incompatible with IncW plasmids, suggesting that the ori2 or ori3 region contains the IncW determinant. We have cloned a replication initiation protein (RepB) that is necessary for ori2 and ori3 to function. This Rep protein is distinct from RepA, which is necessary for ori1. Thus, pJD4 is unique because it is the smallest plasmid characterized containing three origins of replication and two unique Rep proteins.

Antimicrobial susceptibility of Neisseria gonorrhoeae isolates from three Caribbean countries: Trinidad, Guyana, and St. Vincent.

BACKGROUND: The percentage of Neisseria gonorrhoeae isolates resistant to antimicrobial agents commonly used for treatment is unknown in many Caribbean countries. GOAL: To determine the antimicrobial susceptibility of N gonorrhoeae isolates from Trinidad (144 isolates), Guyana (70 isolates), and St. Vincent (68 isolates) so baseline data can be established for further studies, and to assist in establishing effective treatment guidelines. STUDY DESIGN: Consecutive urethral and endocervical specimens from several clinics were collected and identified as N gonorrhoeae. Isolates of N gonorrhoeae were tested for their susceptibility to penicillin, tetracycline, ceftriaxone, ciprofloxacin, spectinomycin, and azithromycin. The presumptive identification of penicillinase-producing N gonorrhoeae and/or tetracycline-resistant N gonorrhoeae isolates based on MIC was confirmed by plasmid and tetM content analysis. RESULTS: High percentages of penicillin and/or tetracycline resistance were observed in N gonorrhoeae isolates from Guyana (92.9%), St. Vincent (44.1%), and Trinidad (42.4%). Isolates from all three countries were susceptible to ceftriaxone, ciprofloxacin, and spectinomycin. One penicillinase-producing N gonorrhoeae/tetracycline-resistant N gonorrhoeae from Guyana had an MIC of 0.5 microg/l to ciprofloxacin. This and nine other isolates from Guyana also were resistant to azithromycin (defined as MIC > or = 2.0 microg/ml) as well as penicillin and tetracycline. A reduced susceptibility to azithromycin was displayed by 16% of the isolates from St. Vincent and 72% of the isolates from Guyana (MIC, 0.25-1.0 microg/ml). Most penicillinase-producing N gonorrhoeae isolates carried Africa-type plasmids (61/90), with 28 of 90 having Toronto-type plasmids and a single isolate carrying an Asia-type plasmid. The tetM determinant in tetracycline-resistant N gonorrhoeae isolates was predominantly of the Dutch type (68/91). CONCLUSIONS: The high prevalence of N gonorrhoeae isolates from 3 of 21 English- and Dutch-speaking Caricom countries in the Caribbean with either plasmid-mediated or chromosomal resistance to penicillin and tetracycline supports international observations that these drugs should not be used to treat gonococcal infections. The detection of isolates with reduced susceptibility to drugs such as azithromycin, which currently are recommended for treatment in the region, attest to the importance of the continued monitoring of gonococcal antimicrobial susceptibility for the maintenance of effective treatment guidelines.

Reduced susceptibility to azithromycin and high percentages of penicillin and tetracycline resistance in Neisseria gonorrhoeae isolates from Manaus, Brazil, 1998.

BACKGROUND: The identification of Neisseria gonorrhoeae isolates resistant to antimicrobial agents currently recommended for the treatment of gonococcal infections continues to escalate globally. Thus, in some areas, resistance to fluoroquinolone drugs is commonplace; several reports document resistance to third-generation cephalosporins, and the sporadic isolation of spectinomycin-resistant isolates continues unabated. Gonococcal resistance to azithromycin, an antibiotic used for the primary treatment of gonococcal infections in some Latin American countries, also has been described. Because the prevalence of resistant isolates is insufficiently documented in many areas of Latin America, the efficacy of locally recommended therapies for gonococcal infections is often unknown. GOAL: To determine the antimicrobial susceptibility and strain types of N gonorrhoeae isolates collected in Manaus, Brazil. These data will establish antimicrobial susceptibility baseline data for the region as a reference point for future surveillance. STUDY DESIGN: Consecutive N gonorrhoeae isolates from urethral and endocervical specimens were collected and examined for identity, antimicrobial susceptibility, and strain type (plasmid content, tetM type, auxotype, and serovar). RESULTS: Most of the isolates (65/81; 85.2%) were resistant to tetracycline, penicillin, or both, with the majority (n = 62) carrying plasmid-mediated resistance to tetracycline (tetracycline-resistant N gonorrhoeae [TRNG]). All of the TRNG contained the Dutch-type tetM plasmid, and 18 were A/S class NR/IA-02. Penicillinase-producing N gonorrhoeae comprised 8.2% (7/81) of the isolates. Of these seven isolates, four also were TRNG, and two carried chromosomal resistance to tetracycline. The isolates were susceptible to ciprofloxacin, spectinomycin, and ceftriaxone. However, 23 isolates were characterized by reduced susceptibility to azithromycin (MIC, 0.25-0.5 microg/ml), and one isolate had reduced susceptibility to ciprofloxacin (MIC, 0.25 microg/ml). CONCLUSIONS: This study supports the continued use of third-generation cephalosporins, spectinomycin, and fluoroquinolone drugs for the primary treatment of gonococcal infections in Manaus. The occurrence of isolates with reduced susceptibility to azithromycin and ciprofloxacin underscores the importance of ongoing antimicrobial susceptibility monitoring to support decisions regarding appropriate drugs for the treatment of gonococcal infections.

Expression of Neisseria gonorrhoeae cell division genes ftsZ, ftsE and minD is influenced by environmental conditions.

The activity of the promoter regions of the cell division genes ftsZ, ftsE, minC, minD and minE from Neisseria gonorrhoeae (Ng) was studied under different environmental conditions using lacZ translational fusions. The promoters of the minNg genes have not been previously determined and we identified promoter regions upstream of each gene (minCp, minDp and minEp). We determined that minDp had the strongest activity. Expression of the promoter regions of ftSZ(Ng) and ftsE(Ng), which we had previously identified, as well as minD(Ng), were then studied under conditions reflecting the environment of the genitourinary tract. These conditions included anaerobiosis, presence of isoleucine or urea (3 mM and 400 mM, respectively) and acidity of pH 6. Both beta-galactosidase expression and northern blot analysis indicated that all three genes were upregulated under anaerobiosis. The addition of isoleucine as well as media at pH 6 did not have any significant effects on the promoter activity of these genes while the presence of urea significantly decreased ftsZ(Ng) promoter activity. The expression of the minD(Ng) promoter region was analyzed during different growth phases and shown to follow the growth behavior of the culture. By contrast, the ftSZ(Ng) promoter activity continued to rise after the onset of the stationary phase. When gonococcal ftsZ promoter 1, (Pz1) was altered by site-directed mutagenesis, a significant decrease in the expression of ftsZ(Ng) was observed under both aerobic and anaerobic conditions. These data infer that gonococci regulate their cell division in response to different environments.

Genomic, transcriptional and phenotypic analysis of ftsE and ftsX of Neisseria gonorrhoeae.

Although ftsE and ftsX are not universally present in bacteria, they are present in various Neisseria species as determined by Southern hybridization. The ftsE and ftsX genes of Neisseria gonorrhoeae (Ng) CH811 were cloned, sequenced and were shown to be co-transcribed from two promoters (P(E)1 and P(E)2) which were identified upstream of ftsE(Ng) by primer extension. Sequence analysis of FtsE(Ng) and alignment with other FtsE indicated that it contained the conserved motifs of ABC domains while sequence alignment of FtsX(Ng) with other published FtsX sequences predicted that they all contain four transmembrane segments and a conserved motif (Leu-hydrophobic aa-Gly-Ala/Gly) which may prove to be important for FtsX function. The viability of ftsE(Ng) and ftsX(Ng) mutants that were constructed by insertional inactivation indicated that these genes are not essential. The role of FtsE and FtsX is controversial. Analysis of ftsE(Ng) and ftsX(Ng) mutants by transmission electron microscopy showed that both exhibited morphological abnormalities indicative of defective division sites and in some cases aberrant condensation of DNA.

Sequence analysis of the family of penicillinase-producing plasmids of Neisseria gonorrhoeae.

The exact nature of the sequence differences between the medically important family of gonococcal penicillinase-producing plasmids has been ascertained. The entire DNA sequence of the Asia-type plasmid, pJD4, demonstrated that it is 7426 bp and contains two direct repeats (DR30) that are implicated in the formation of deletion variant plasmids, such as the Africa-type plasmid. We have identified putative DnaA and IHF binding sites, various open reading frames that are thought to specify functional proteins, and some important DNA sequences involved with conjugative transfer of gonococcal beta-lactamase plasmids. The deletion in the Africa-type plasmid is 1827 bp and one of the DR30 repeats is also missing. The deletion in the Rio-type plasmid and several Toronto-type plasmids was determined to be 2273 bp and the sequence spanning the deletion was identical irrespective of geographic or temporal origin. The &Ncirc;imes-type plasmid is an Africa-type plasmid and also contains an IS5 insertion sequence. Since IS5 has not been identified in gonococcal isolates, we suggest that this sequence may have been inserted after the original gonococcal plasmid was transformed into Escherichia coli. The New Zealand plasmid is an Asia-type plasmid that contains an endogenous tandem duplication of 1883 bp and the direct DR2 is implicated in this duplication. The nature of the defined truncation of Tn2 present in the various plasmids is also discussed.

Importance of drug resistance in gonococci: from mechanisms to monitoring.

Neisseria gonorrhoeae isolates continue to develop an impressive arsenal of resistance mechanisms to antimicrobial agents, including resistance to some of the antibiotics presently recommended for the treatment of gonococcal infections.

Aminopeptidase activities in Peptostreptococcus spp. are statistically correlated to gelatin hydrolysis.

One hundred Peptostreptococcus isolates from five species were assessed for their ability to hydrolyze gelatin. Most Peptostreptococcus magnus (95.8%) and Peptostreptococcus micros isolates (79.0%) hydrolyzed gelatin in contrast to Peptostreptococcus asaccharolyticus (8.0%), Peptostreptococcus anaerobius (10.0%), and Peptostreptococcus prevotii isolates (16.7%). Gelatin hydrolysis in Peptostreptococcus magnus and Peptostreptococcus micros isolates correlated (r = 0.80; P = 0.0019) with more aminopeptidases produced than Peptostreptococcus asaccharolyticus, Peptostreptococcus anaerobius, or Peptostreptococcus prevotii. The five species were further classified into three groups using the extended Tukey test (P < 0.0001) based on the mean percentage of aminopeptidases produced by each species with Peptostreptococcus magnus and Peptostreptococcus micros belonging to group I, Peptostreptococcus asaccharolyticus and Peptostreptococcus prevotii belonging to group II, and Peptostreptococcus anaerobius forming group III. An analysis of possible proteolytic activity of four selected Peptostreptococcus magnus isolates indicated that only 5 of 11 substrates were hydrolyzed as compared to a control isolate of Porphyromonas gingivalis W83, which had a strong proteolytic profile. Therefore, gelatin hydrolysis by Peptostreptococcus spp., in particular Peptostreptococcus magnus and Peptostreptococcus micros, is probably due to a variety of aminopeptidases rather than proteinases.

Mapping antibiotic-resistant Neisseria gonorrhoeae isolates in Metropolitan Toronto: Issues of scale, positional accuracy and confidentiality.

The primary objective of this paper was to investigate the methodological implications of mapping Neisseria gonorrhoeae using the partial three-digit postal code instead of the complete six-digit postal code. The reporting locations of N gonorrhoeae isolates submitted from hospitals, doctor's offices, private and provincial laboratories, and sexually transmitted disease (STD) clinics were used as a model. Specifically, the paper focused on variations in geographical distributions of STD data when mapped at different aggregations of postal code data and at different map scales. Such variations are of importance to those who analyze the spatial epidemiology of STDs, and the accessibility and use of health care services. This analysis showed that three-digit postal codes are useful in summarizing overall geographic distributions, but greatly reduce positional accuracy, which can lead to inaccurate delineation of service areas and populations served. The six-digit postal code is more appropriate for detailed analysis addressing behavioural issues. The analysis demonstrated that six-digits can be used without breaching individual confidentiality.

Phylogenetic analysis of carbamoylphosphate synthetase genes: complex evolutionary history includes an internal duplication within a gene which can root the tree of life.

Carbamoylphosphate synthetase (CPS) catalyzes the first committed step in pyrimidine biosynthesis, arginine biosynthesis, or the urea cycle. Organisms may contain either one generalized or two specific CPS enzymes, and these enzymes may be heterodimeric (encoded by linked or unlinked genes), monomeric, or part of a multifunctional protein. In order to help elucidate the evolution of CPS, we have performed a comprehensive phylogenetic analysis using the 21 available complete CPS sequences, including a sequence from Sulfolobus solfataricus P2 which we report in this paper. This is the first report of a complete CPS gene sequence from an archaeon, and sequence analysis suggests that it encodes an enzyme similar to heterodimeric CPSII. We confirm that internal similarity within the synthetase domain of CPS is the result of an ancient gene duplication that preceded the divergence of the Bacteria, Archaea, and Eukarya, and use this internal duplication in phylogenetic tree construction to root the tree of life. Our analysis indicates with high confidence that this archaeal sequence is more closely related to those of Eukarya than to those of Bacteria. In addition to this ancient duplication which created the synthetase domain, our phylogenetic analysis reveals a complex history of further gene duplications, fusions, and other events which have played an integral part in the evolution of CPS.

Utility of ribotyping, restriction endonuclease analysis and pulsed-field gel electrophoresis to discriminate between isolates of Neisseria gonorrhoeae of serovar IA-2 which require arginine, hypoxanthine or uracil for growth.

Neisseria gonorrhoeae isolates that require arginine--i.e., either citrulline (C), or ornithine (O)--uracil (U) and hypoxanthine (H) have generally been considered to be similar when characterised by auxotype, serovar and plasmid content. The MICs of penicillin, tetracycline, erythromycin, spectinomycin, cefoxitin and ceftriaxone for 552 isolates belonging to serovar IA-2 with these phenotypes were found to be similar. Therefore, restriction fragment length polymorphism analysis of rRNA genes (ribotyping), restriction enzyme (RE) analysis of chromosomal DNA, and pulsed-field gel electrophoresis (PFGE) were evaluated to determine whether these isolates could be distinguished by molecular methods. A subset of 27 isolates of N. gonorrhoeae that were OUH-requiring, CUH-requiring or OH-requiring, belonged to serovar IA-2 and carried a 2.6-MDa plasmid, were selected for further study. Based on the RE analysis of SmaI-digested genomic DNA, the 27 isolates fell into a single RE pattern, five ribotypes and 17 PFGE profiles which did not correlate with the specific arginine-requiring subtypes of these isolates. Each ribotype varied by the presence of only a single fragment, which was of a different size in each pattern, and 17 (63%) of the 27 isolates belonged to ribotype I. PFGE yielded the highest level of discrimination with 17 different profiles.

Differentiation of Neisseria gonorrhoeae isolates requiring proline, citrulline, and uracil by plasmid content, serotyping, and pulsed-field gel electrophoresis.

A combination of DNA macrorestriction analysis using pulsed-field gel electrophoresis and a serotyping method using three panels of monoclonal antibody was used to discriminate 43 epidemiologically unrelated Neisseria gonorrhoeae isolates requiring proline, citrulline, and uracil (PCU-) into 35 groups. This indicates that PCU- isolates of N. gonorrhoeae are not clonal.