Genome-wide maps of highly-similar intrachromosomal repeats that mediate ectopic recombination in three human genome assemblies.

Repeated sequences spread throughout the genome play important roles in shaping the structure of chromosomes and facilitating the generation of new genomic variation. Through a variety of mechanisms, repeats are involved in generating structural rearrangements such as deletions, duplications, inversions, and translocations, which can have the potential to impact human health. Despite their significance, repetitive regions including tandem repeats, transposable elements, segmental duplications, and low-copy repeats remain a challenge to characterize due to technological limitations inherent to many sequencing methodologies. We performed genome-wide analyses and comparisons of direct and inverted repeated sequences in the latest available human genome reference assemblies including GRCh37 and GRCh38 and the most recent telomere-to-telomere alternate assembly (T2T-CHM13). Overall, the composition and distribution of direct and inverted repeats identified remains similar among the three assemblies but we observed an increase in the number of repeated sequences detected in the T2T-CHM13 assembly versus the reference assemblies. As expected, there is an enrichment of repetitive regions in the short arms of acrocentric chromosomes, which had been previously unresolved in the human genome reference assemblies. We cross-referenced the identified repeats with protein-coding genes across the genome to identify those at risk for being involved in genomic disorders. We observed that certain gene categories, such as olfactory receptors and immune response genes, are enriched among those impacted by repeated sequences likely contributing to human diversity and adaptation. Through this analysis, we have produced a catalogue of direct and inversely oriented repeated sequences across the currently three most widely used human genome assemblies. Bioinformatic analyses of these repeats and their contribution to genome architecture can reveal regions that are most susceptible to genomic instability. Understanding how the architectural genomic features of repeat pairs such as their homology, size and distance can lead to complex genomic rearrangement formation can provide further insights into the molecular mechanisms leading to genomic disorders and genome evolution. Author summary: This study focused on the characterization of intrachromosomal repeated sequences in the human genome that can play important roles in shaping chromosome structure and generating new genomic variation in three human genome assemblies. We observed an increase in the number of repeated sequence pairs detected in the most recent telomere-to-telomere alternate assembly (T2T-CHM13) compared to the reference assemblies (GRCh37 and GRCh38). We observed an enrichment of repeats in the T2T-CHM13 acrocentric chromosomes, which had been previously unresolved. Importantly, our study provides a catalogue of direct and inverted repeated sequences across three commonly used human genome assemblies, which can aid in the understanding of genomic architecture instability, evolution, and disorders. Our analyses provide insights into repetitive regions in the human genome that may contribute to complex genomic rearrangements.

Tactile stimulation prevents disruptions in male rat copulatory behavior induced by artificial rearing.

Early life social interactions in gregarious mammals provide an important source of stimulation required for the development of species-typical behaviors. In the present study, complete deprivation of maternal and littermate contact through artificial rearing was used to examine the role of early social stimulation on copulatory behavior and the ejaculate in adult rats. We found that artificially reared naïve male rats were sexually motivated; nevertheless, they did not acquire the level of sexual experience that typically occurs during copulatory training. Disrupted expression of sexual experience of artificially reared rats was demonstrated by an inconsistent pattern of ejaculatory behavior across training tests. Artificial tactile stimulation applied during isolation prevented this disruption and rats achieved ejaculation in most copulatory tests. Despite the irregularity of ejaculatory behavior in isolated rats, their sperm count and seminal plug were similar to control maternally reared (sexually experienced) and artificially-reared rats that received tactile stimulation. These results suggest that tactile sensory information provided by the mother and/or littermates to the offspring is crucial for the development of copulatory behavior. The absence of social and/or tactile stimulation during early life compromises the ability of male rats to gain sexual experience in adulthood.

Impact of orange essential oil on enteric methane emissions of heifers fed bermudagrass hay.

In this study, the effects of orange essential oil (OEO) on the rumen fermentation, nutrient utilization, and methane (CH4) emissions of beef heifers fed a diet of bermudagrass (Cynodon dactylon) were examined. In addition, in vitro and in situ experiments were conducted. The in vitro experiment consisted of three treatments: control (CTL, no OEO), OEO1 (0.25% OEO), and OEO2 (0.5% OEO). The forage to concentrate ratio was 70:30 (dry matter [DM] basis) in all treatments. No changes in pH, proportions of volatile fatty acids, and the acetate:propionate ratio were observed (P > 0.05). The addition of 0.25% OEO resulted in a reduction in CH4 production (mL/g) relative to the control (P < 0.05). In the in situ experiment, 5 g of total mixed ration (CTL, OEO1, and OEO2) were incubated for 6, 12, 24, 48, and 72 h. Potential and effective degradability were not affected by OEO supplementation (P > 0.05). In the in vivo study, six crossbred beef heifers (Bos indicus × Bos taurus), fitted with rumen cannulas, were assigned to three different treatments: no additive (CTL), 0.25% OEO (OEO1), and 0.5% OEO (OEO2) in a replicated 3 × 3 Latin square (21-day periods). Heifers were fed at 2.8% body weight. In vivo CH4 production was measured in open-circuit respiration chambers. Reductions in gross energy consumption, apparent total tract digestibility, and rumen valerate concentration were observed for OEO2 compared to the control (P < 0.05). Additionally, decreases in CH4 emissions (g/day; P < 0.05) and CH4 (MJ gross energy intake/day; P < 0.05) were observed in response to supplementation of 0.5% OEO as compared to the CTL treatment. Thus, supplementation of 0.5% OEO reduced CH4 emissions (g/day) by 12% without impacting the DM intake of heifers fed bermudagrass hay as a basal ration.

Threshold for copulation-induced analgesia varies according to the ejaculatory endophenotypes in rats.

Analgesia may be modulated by multiple internal and external factors. In prior studies, copulatory-induced analgesia was demonstrated using the vocalization threshold to tail shock (VTTS) in male and female rats. Three ejaculatory endophenotypes have been characterized in male Wistar rats based upon their ejaculation latency (EL). Since intromissions and ejaculations produce analgesia, and these copulatory patterns are performed with different frequency depending on the male's ejaculatory endophenotype, we hypothesized that copulation-induced analgesia would vary in relation to these endophenotypes. In the present study, we used three groups according to the EL (medians): rapid ejaculators (236 s; n = 21), intermediate ejaculators (663.2 s; n = 20) and sluggish ejaculators (1582.2 s; n = 8). Our aim was to evaluate whether copulation-induced analgesia is related to the ejaculatory endophenotypes during two consecutive ejaculatory series (EJS). In the first EJS, the VTTS of the rapid ejaculators was significantly higher than that of intermediate and sluggish rats. At the onset of the second EJS, the VTTS of the rapid and intermediate ejaculators was significantly higher than that of the sluggish rats. No differences in VTTS were observed during the first or second post-ejaculatory intervals among the three groups. These findings provide evidence that the more intromissions that occurred per unit time, the higher was the level of analgesia.

Effect of Chitosan and Naringin on Enteric Methane Emissions in Crossbred Heifers Fed Tropical Grass.

In order to meet consumer needs, the livestock industry is increasingly seeking natural feed additives with the ability to improve the efficiency of nutrient utilization, alternatives to antibiotics, and mitigate methane emissions in ruminants. Chitosan (CHI) is a polysaccharide with antimicrobial capability against protozoa and Gram-positive and -negative bacteria, fungi, and yeasts while naringin (NA) is a flavonoid with antimicrobial and antioxidant properties. First, an in vitro gas production experiment was performed adding 0, 1.5, 3.0 g/kg of CHI and NA under a completely randomized design. The substrate containing forage and concentrate in a 70:30 ratio on a dry matter (DM) basis. Compounds increased the concentration of propionic acid, and a significant reduction in methane production was observed with the inclusion of CHI at 1.5 g/kg in in vitro experiments (p < 0.001). In a dry matter rumen degradability study for 96 h, there were no differences in potential and effective degradability. In the in vivo study, six crossbred heifers fitted with rumen cannulas were assigned to a 6 × 6 Latin square design according to the following treatments: control (CTL), no additive; chitosan (CHI1, 1.5 g/kg DMI); (CHI2, 3.0 g/kg DMI); naringin (NA1, 1.5 g/kg DMI); (NA2, 3.0 g/kg DMI) and a mixture of CHI and NA (1.5 + 1.5 g/kg DMI) given directly through the rumen cannula. Additives did not affect rumen fermentation (p > 0.05), DM intake and digestibility of (p > 0.05), and enteric methane emissions (p > 0.05). CHI at a concentration of 1.5 g/kg DM in in vitro experiments had a positive effect on fermentation pattern increasing propionate and reduced methane production. In contrast, in the in vivo studies, there was not a positive effect on rumen fermentation, nor in enteric methane production in crossbred heifers fed a basal ration of tropical grass.

Role of Secondary Plant Metabolites on Enteric Methane Mitigation in Ruminants.

The rumen microbiome plays a fundamental role in all ruminant species, it is involved in health, nutrient utilization, detoxification, and methane emissions. Methane is a greenhouse gas which is eructated in large volumes by ruminants grazing extensive grasslands in the tropical regions of the world. Enteric methane is the largest contributor to the emissions of greenhouse gases originating from animal agriculture. A large variety of plants containing secondary metabolites [essential oils (terpenoids), tannins, saponins, and flavonoids] have been evaluated as cattle feedstuffs and changes in volatile fatty acid proportions and methane synthesis in the rumen have been assessed. Alterations to the rumen microbiome may lead to changes in diversity, composition, and structure of the methanogen community. Legumes containing condensed tannins such as Leucaena leucocephala have shown a good methane mitigating effect when fed at levels of up to 30-35% of ration dry matter in cattle as a result of the effect of condensed tannins on rumen bacteria and methanogens. It has been shown that saponins disrupt the membrane of rumen protozoa, thus decreasing the numbers of both protozoa and methanogenic archaea. Trials carried out with cattle housed in respiration chambers have demonstrated the enteric methane mitigation effect in cattle and sheep of tropical legumes such as Enterolobium cyclocarpum and Samanea saman which contain saponins. Essential oils are volatile constituents of terpenoid or non-terpenoid origin which impair energy metabolism of archaea and have shown reductions of up to 26% in enteric methane emissions in ruminants. There is emerging evidence showing the potential of flavonoids as methane mitigating compounds, but more work is required in vivo to confirm preliminary findings. From the information hereby presented, it is clear that plant secondary metabolites can be a rational approach to modulate the rumen microbiome and modify its function, some species of rumen microbes improve protein and fiber degradation and reduce feed energy loss as methane in ruminants fed tropical plant species.

Increase in Milk Yield from Cows through Improvement of Forage Production Using the N2-Fixing Legume Leucaena leucocephala in a Silvopastoral System.

The objective was to evaluate milk production, N2-fixation and N transfer, forage yield and composition (under two cutting intervals) in a silvopastoral system (SPS) with Leucaena leucocephala-Megathyrsus maximus and M. maximus-monoculture (MMM) with crossbred cows in a completely randomized design. Forage yield in the SPS was 6490 and 6907 kg DM ha-1 for cutting intervals (CI) of 35 and 50 days. Forage yield for the MMM was 7284 and 10,843 kg DM ha-1, and forage crude protein (CP) was 29.0% and 26.1% for L. leucocephala, harvested at 35 and 50 days, respectively. CP for the associated M. maximus was 9.9% and 7.8% for CI 35 and 50 days, respectively, and for MMM was 7.4% and 8.4%, harvested at 35 and 50 days. Milk production was 4.7 kg cow-1 day-1 for cows grazing MMM and 7.4 kg cow-1 day-1 under SPS. Nitrogen fixation in L. leucocephala (%Ndfa) was estimated to be 89% and 95%, at 35 and 50 days, with an N2 transfer to the associated grass of 34.3% and 52.9%. SPS has the potential to fix and transfer important amounts of N2 to the associated grass, and increase forage CP content and milk production.

Influence of energy supplementation on dietary nitrogen utilization and milk production in cows fed foliage of Leucaena leucocephala.

The aim of the study was to assess the effect of four energy supplements (two highly fermentable; two starch-based carbohydrates) on blood urea nitrogen (BUN), urinary urea excretion, and milk yield, in dual-purpose cows fed foliage of Leucaena leucocephala (Leucaena). Five Holstein-Zebu cows with 450 kg body weight in their second third of lactation were used in a 5 × 5 Latin square design. Cows were fed (dry basis) a mixture of 45% Leucaena and 55% Pennisetum purpureum grass. Treatments were supplementation with (i) sugarcane molasses (Mo), (ii) sorghum grain (So), (iii) fresh citrus pulp (CitP) or (iv) rice polishing (RP), all of them incorporated into the diet at 25 MJ of ME/cow/day. There was a control group (Cont) without energy supplementation. The study comprised five periods of 20 days (15 days adaptation, 5 days measurements). Dry matter intake (kg/day) was lower (P < 0.05) for Cont (9.4) compared with Mo (12.1), So (12.0), CitP (11.9) and RP (11.9) but no difference was observed among energy supplements (P > 0.05). Milk yield (kg/day) was higher (P < 0.05) in cows supplemented with starch supplements (4.7 for So; 4.9 for RP) compared with Cont (3.3). Milk yield from highly fermentable supplements (Mo and CitP) did not differ (P > 0.05) from Cont or other treatments. Milk protein, fat and lactose were not different among treatments (P > 0.05). Blood urea nitrogen and urinary urea excretion were both reduced (P < 0.05) by energy supplementation. Urinary urea excretion was not different (P > 0.05) among cows fed different sources of energy. It is concluded that in dual-purpose cows fed Leucaena foliage, supplementation with sugarcane molasses, citrus pulp or rice polishing reduced blood urea nitrogen and urinary urea excretion. Milk yield was increased by sorghum and rice polishing whereas energy supplementation did not affect milk composition.

Effect of Dried Leaves of Leucaena leucocephala on Rumen Fermentation, Rumen Microbial Population, and Enteric Methane Production in Crossbred Heifers.

The effects of dietary inclusion of dried Leucaena leucocephala leaves (DLL) on nutrient digestibility, fermentation parameters, microbial rumen population, and production of enteric methane (CH4) in crossbred heifers were evaluated. Four heifers were used in a 4 × 4 Latin square design consisting of four periods and four levels of inclusion of DLL: 0%, 12%, 24%, and 36% of dry matter (DM) intake. Results showed that DM intake (DMI), organic matter intake, and gross energy intake (GEI) were similar (p > 0.05) among treatments. Apparent digestibility of organic matter, neutral detergent fiber, and energy decreased with increasing levels of DLL in the ration (p < 0.05). In contrast, digestible crude protein (CP) was higher (p < 0.05) in treatments with 12% and 24% DM of DLL. The inclusion of DLL did not affect (p > 0.05) rumen pH and total volatile fatty acids. Rumen microbial community was not affected (p > 0.05) by treatment. There was a linear reduction (p < 0.05) in CH4 emissions as the levels of DLL in the ration were increased. Results of this study suggest that an inclusion of 12% DM of ration as DLL enhances digestible CP and reduces daily production of enteric CH4 without adversely affecting DMI, rumen microbial population, and fermentation parameters.

The Role of Chitosan as a Possible Agent for Enteric Methane Mitigation in Ruminants.

Livestock production is a main source of anthropogenic greenhouse gases (GHG). The main gases are CH4 with a global warming potential (GWP) 25 times and nitrous oxide (N2O) with a GWP 298 times, that of carbon dioxide (CO2) arising from enteric fermentation or from manure management, respectively. In fact, CH4 is the second most important GHG emitted globally. This current scenario has increased the concerns about global warming and encouraged the development of intensive research on different natural compounds to be used as feed additives in ruminant rations and modify the rumen ecosystem, fermentation pattern, and mitigate enteric CH4. The compounds most studied are the secondary metabolites of plants, which include a vast array of chemical substances like polyphenols and saponins that are present in plant tissues of different species, but the results are not consistent, and the extraction cost has constrained their utilization in practical animal feeding. Other new compounds of interest include polysaccharide biopolymers such as chitosan, mainly obtained as a marine co-product. As with other compounds, the effect of chitosan on the rumen microbial population depends on the source, purity, dose, process of extraction, and storage. In addition, it is important to identify compounds without adverse effects on rumen fermentation. The present review is aimed at providing information about chitosan for dietary manipulation to be considered for future studies to mitigate enteric methane and reduce the environmental impact of GHGs arising from livestock production systems. Chitosan is a promising agent with methane mitigating effects, but further research is required with in vivo models to establish effective daily doses without any detrimental effect to the animal and consider its addition in practical rations as well as the economic cost of methane mitigation.

Effect of grazing cows in an intensive silvopastoral system with Leucaena leucocephala on Panela cheese properties: yield, composition, fatty acid profile and sensory acceptability.

Yield, chemical composition, fatty acid profile, and sensory acceptability of Panela cheese produced from cows grazing in an intensive silvopastoral system (ISS) with Leucaena leucocephala and Cynodon nlemfuensis were evaluated and compared with Panela cheese from cows grazing a monoculture system (MS) of C. nlemfuensis only. The experiment lasted for 9 weeks in a tropical area in Mexico using ten crossbred cows (30-90 days of milking) assigned homogenously as five cows in each experimental group. No significant differences were found between the two systems for milk and cheese gross composition. Panela cheese from ISS showed lower content of the hypercholesterolemic fatty acids, accompanied with higher content of omega-3, omega-6 and polyunsaturated fatty acids. In addition, Panela cheese from ISS showed higher preference for the attributes of appearance, texture, flavor, and overall acceptability. It is concluded that Panela cheese from cows grazing in ISS has better acceptability and nutritional properties than that produced from MS with grass only.

Effect of condensed tannins from Leucaena leucocephala on rumen fermentation, methane production and population of rumen protozoa in heifers fed low-quality forage.

OBJECTIVE: The aim of the experiment was to assess the effect of increasing amounts of Leucaena leucocephala forage on dry matter intake (DMI), organic matter intake (OMI), enteric methane production, rumen fermentation pattern and protozoa population in cattle fed Pennisetum purpureum and housed in respiration chambers. METHODS: Five crossbred heifers (Bos taurus×Bos indicus) (BW: 295±6 kg) were fed chopped P. purpureum grass and increasing levels of L. leucocephala (0%, 20%, 40%, 60%, and 80% of dry matter [DM]) in a 5×5 Latin square design. RESULTS: The voluntary intake and methane production were measured for 23 h per day in respiration chambers; molar proportions of volatile fatty acids (VFAs) were determined at 6 h postprandial period. Molar concentration of VFAs in rumen liquor were similar (p>0.05) between treatments. However, methane production decreased linearly (p<0.005), recording a maximum reduction of up to ~61% with 80% of DM incorporation of L. leucocephala in the ration and no changes (p>0.05) in rumen protozoa population were found. CONCLUSION: Inclusion of 80% of L. leucocephala in the diet of heifers fed low-quality tropical forages has the capacity to reduce up to 61.3% enteric methane emission without affecting DMI, OMI, and protozoa population in rumen liquor.

Ovarian activity and estrus behavior in early postpartum cows grazing Leucaena leucocephala in the tropics.

The legume Leucaena leucocephala (Leucaena) is widely used to supplement forage in silvopastoral livestock systems in Latin America. Little is known about its possible effects on the cow reproductive dynamic. The aim was to evaluate the effect of Leucaena foliage intake on re-establishment of ovarian activity and estrus behavior in early postpartum (7-90 days) cows. Twenty-four multiparous Bos taurus × Bos indicus cows were divided into two homogenous groups and assigned to one of two treatments: a silvopastoral system (SS, n = 12), consisting of an association of Cynodon nlemfuensis grass and L. leucocephala; and a control system (CS, n = 12), consisting of C. nlemfuensis alone. Intake of Leucaena in the SS ranged from 3.80 to 6.43 kg DM/cow/day. Plasma mimosine concentrations ranged from 1270 to 1530 µg/mL, and those for 2,3-dihydroxypyridine (DHP) from 147 to 729 µg/mL. No 3,4-DHP was detected in plasma. No difference (P > 0.05) between treatments was observed for the number of cows exhibiting small, medium, or dominant follicles, or estrus behavior. The number of cows which re-established ovarian cyclicity (n = 6) was lower (P < 0.05) in the SS than in the CS (n = 9). Corpus luteum lifespan was longer (P < 0.05) in the SS than in the CS. Intake of Leucaena affected the number of cows exhibiting ovarian cyclicity and extended corpus luteum life, but did not affect follicular development and estrus behavior.

Effects of energy supplementation on productivity of dual-purpose cows grazing in a silvopastoral system in the tropics.

The aim of the present work was to evaluate milk yield, postpartum (pp) ovarian activity and pregnancy rate in dual-purpose cows grazing Cynodon nlemfuensis and browsing L. leucocephala, with or without energy supplementation. Twenty-four Bos taurus × B. indicus cows were divided in two groups from calving to 70 days post-calving: supplemented group (SG) with ground sorghum grain offered at 0.4% of live weight at calving and control group (CG) without supplement. There was a trend for milk yield (kg day(-1)) to be greater (p = 0.08) for SG (10.55 ± 0.51) compared to CG (9.53 ± 0.61), although without differences in fat (0.42 ± 0.02 vs. 0.38 ± 0.03 kg day(-1)), protein (0.29 ± 0.02 vs. 0.29 ± 0.02 kg day(-1)) or lactose (0.49 ± 0.02 vs. 0.49 ± 0.03 kg day(-1)) concentration. Populations of large, medium and small follicles were similar between treatments. Percentage of cows which showed corpus luteum tended to be greater in SG (50%), compared to CG (33%). Supplemented cows tended to have a shorter calving-first corpus luteum interval (40 ± 10 vs. 51 ± 10 days) and had a significantly higher (χ (2) = 0.03) pregnancy rate (42% vs. 0%). It is concluded that energy supplementation helped to improve ovarian activity and pregnancy rate. Since supplementation did not avoid loss of body condition, the higher pregnancy rate in SG suggests beneficial effects of supplementation probably mediated by metabolic hormones.

Energetic efficiency of milk synthesis in dual-purpose cows grazing tropical pastures.

The aim of this study was to assess the energetic efficiency of milk synthesis by grazing dual-purpose cows with or without a starch-based supplement in tropical South Mexico. Forty-six Holstein × Zebu cows were used in a 2 × 2 × 2 factorial design. Factors analysed were diet (supplemented, unsupplemented), age (young: 1-2 calvings, mature: >3 calvings) and day of lactation (21 and 84 days post-calving). The supplement represented about 30% of estimated dry matter (DM) intake. Grass intake was measured using the n-alkane technique at 21 and 84 days post-calving when calculations of efficiency were performed. Efficiency for milk synthesis was reported as feed conversion efficiency (FCE, kilograms of milk per kilogram of DM intake), gross energetic efficiency (GEE, milk energy output/metabolisable energy (ME) intake) and efficiency of ME use for lactation (k(l), adjusted to zero energy balance). There were no interactions between factors. FCE and GEE were not different between diets, but supplemented cows had a lower (p < 0.01) k(l) value (0.62) than unsupplemented cows (0.67), suggesting a diverted partition of nutrients towards body tissue. Mature cows were more efficient (p < 0.001) than young cows in terms of FCE (1.13 vs 0.87) and GEE (0.34 vs 0.26), but equal in terms of k(l) (0.65). FCE (1.10 vs 0.90) and GEE (0.34 vs 0.27) were both higher on day 21 compared with day 84 post-calving, with a trend for a higher k(l) in early lactation. Dual-purpose cows used tropical grasses efficiently for milk synthesis, and higher milk yield observed in supplemented cows was due to a higher intake of nutrients rather than a higher energetic efficiency.