Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease.

In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.

Unlocking gut microbiota potential of dairy cows in varied environmental conditions using shotgun metagenomic approach.

Food security and environmental pollution are major concerns for the expanding world population, where farm animals are the largest source of dietary proteins and are responsible for producing anthropogenic gases, including methane, especially by cows. We sampled the fecal microbiomes of cows from varying environmental regions of Pakistan to determine the better-performing microbiomes for higher yields and lower methane emissions by applying the shotgun metagenomic approach. We selected managed dairy farms in the Chakwal, Salt Range, and Patoki regions of Pakistan, and also incorporated animals from local farmers. Milk yield and milk fat, and protein contents were measured and correlated with microbiome diversity and function. The average milk protein content from the Salt Range farms was 2.68%, with an average peak milk yield of 45 litters/head/day, compared to 3.68% in Patoki farms with an average peak milk yield of 18 litters/head/day. Salt-range dairy cows prefer S-adenosyl-L-methionine (SAMe) to S-adenosyl-L-homocysteine (SAH) conversion reactions and are responsible for low milk protein content. It is linked to Bacteroides fragilles which account for 10% of the total Bacteroides, compared to 3% in the Patoki region. The solid Non-Fat in the salt range was 8.29%, whereas that in patoki was 6.34%. Moreover, Lactobacillus plantarum high abundance in Salt Range provided propionate as alternate sink to [H], and overcoming a Methanobrevibacter ruminantium high methane emissions in the Salt Range. Furthermore, our results identified ruminant fecal microbiomes that can be used as fecal microbiota transplants (FMT) to high-methane emitters and low-performing herds to increase farm output and reduce the environmental damage caused by anthropogenic gases emitted by dairy cows.

Identification of phytase producing bacteria from acidifying Tithonia diversifolia: Potential for ruminant feed development.

Phytate content in feed ingredients can negatively impact digestibility and palatability. To address this issue, it is necessary to study microbes capable of breaking down phytate content. This study aimed to isolate and characterize phytase-producing bacteria from decaying materials rich in phytic acid. The research was conducted in several stages. The first stage involved isolating phytase-producing bacteria from the acidification of Tithonia diversifolia using growth media containing Na-phytate. Bacterial isolates that produced clear zones were then tested for their activity and ability to produce several enzymes, specifically phytase, cellulase, and protease. The next step was to test the morphological characteristics of the bacterial isolate. The final stage of bacterial identification consisted of DNA isolation, followed by PCR amplification of the 16S rRNA gene, DNA sequence homology analysis, and construction of a phylogenetic tree. Based on research, three isolates were found to produce clear phytase zones: isolates R5 (20.3 mm), R7 (16.1 mm) and R8 (31.7 mm). All isolates were able to produce the enzymes phytase (5.45-6.54 U/ml), cellulase (2.60-2.92 U/ml), and protease (22.2-23.4 U/ml). Metagenomic testing identified isolate R7 and R8 as Alcaligenes faecalis and isolate R5 as Achromobacter xylosoxidans. The isolation and characterization of phytase-producing bacteria from Tithonia diversifolia acidification resulted in the identification of two promising candidates that can be applied as sources of phytase producers. Phytase-producing bacteria can be utilized to improve digestibility and palatability in animal feed.

Nutrient digestibility, characteristics of rumen fermentation, and microbial protein synthesis from Pesisir cattle diet containing non-fiber carbohydrate to rumen degradable protein ratio and sulfur supplement.

Background and Aim: To achieve optimal feed efficiency in ruminants, especially Pesisir cattle, it is necessary to maintain a harmonious equilibrium between energy and protein levels within the rumen. Sulfur supplementation can potentially escalate the energy-protein balance in the rumen. The aim of this study was to explore the formulation of ruminant diets by synchronizing rumen degradable protein (RDP) and non-fiber carbohydrate (NFC) while adding sulfur minerals at different levels. Nutrient digestibility, NH3 concentration, volatile fatty acids (VFA) production, microbial protein synthesis (MPS), and methane gas production were assessed. Materials and Methods: We employed a randomized block design with a 2 × 2 × 3 factorial arrangement and examined diverse incubation periods of 6, 24, and 48 h. Treatment consisted of RDP (60% and 65%), NFC (35% and 40%), and sulfur (0%, 0.15%, and 0.3%) levels. In this study, the Tilley and Terry in vitro technique, which used Pesisir cattle's rumen fluid, was employed to assess the digestibility of dry matter, organic matter, acid detergent fiber, neutral detergent fiber, and RDP-Rumen undegradable protein. In addition, it measures various rumen fluid attributes, including pH, NH3, VFA, MPS, and methane gas production. Results: Treatment with a coordinated combination of 65% RDP and 40% NFC combined with 0.15% sulfur supplement yielded significantly improved digestibility and notably reduced methane gas production (p < 0.05). Conclusion: The enhancement in digestibility and reduction in methane gas emissions can be attributed to the interaction of RDP, NFC, and sulfur. Feed digestibility was increased in the 65% RDP treatment with 40% NFC and 0.15% sulfur, along with a decrease in methane gas production.

Effects of herbal plant supplementation on rumen fermentation profiles and protozoan population in vitro.

Background and Aim: In the livestock sector, particularly ruminants, an approach to minimize methane emissions can be carried out through a feeding strategy involving herbal plants containing bioactive compounds that can reduce protozoa and decrease methane gas emissions. The aim of this in vitro study was to analyze the effects of herbal plant supplementation on rumen fermentation, total gas, and methane production, in vitro dry matter digestibility (IVDMD), in vitro organic matter digestibility (IVOMD), and protozoa populations within the rumen. Materials and Methods: Two experiments were conducted in this study. Experiment 1 was conducted to determine the most promising herbal plants capable of increasing total gas production and reducing protozoan populations. Three potential herbals selected in Experiment 1 were continued in Experiment 2 as supplements in the palm kernel meal (PKM)-based ration (70% PKM + 30% herbal plants). Results: Experiment 1 revealed that Eurycoma longifolia (EL), Cola acuminata (CLA), and Cassia alata (CSA) were potential herbal candidates for enhancing total gas production and the percentages of IVDMD and IVOMD. In Experiment 2, supplementation with EL, CLA, and CSA significantly increased IVDMD from 62.84% to 70.15%, IVOMD from 61.61% to 53.18%, and NH3 from 13 mM to 17 mM, as well as reduced partial volatile fatty acids and total gas production. In addition, the methane gas and protozoan populations were reduced. Conclusion: The utilization of EL, CLA, and CSA effectively increased the production of total gas, IVDMD, and IVOMD while reducing methane gas protozoa populations in rumen fermentation compared with the control.

Effectiveness of herbal plants on rumen fermentation, methane gas emissions, in vitro nutrient digestibility, and population of protozoa.

Background and Aim: Herbal plants have the potential to reduce the population of metagonic bacteria and protozoa due to the bioactive compound contained in herbal plants. This study aimed to evaluate the effect of herbal plant supplementation on rumen fermentation characteristics, methane (CH4) gas emissions, in vitro nutrient digestibility, and protozoan populations. Materials and Methods: This study consisted of two stages. Stage I involved determining the potential of herbal plants to increase total gas production (Orskov and McDonald methods) and reduce the protozoan population (Hristov method). Three potential herbs were selected at this stage and used in Stage II as supplements in the palm kernel cake (PKC)-based diet (30% herbal plants + 70% PKC). Proximate and Van Soest analyses were used to determine the chemical composition. In vitro dry matter digestibility (IVDMD), organic matter (IVOMD), and rumen fermentation characteristics were determined using Theodorous method. Conway microdiffusion was used to determine ammonia concentration (NH3). Gas chromatography was used to determine the total and partial volatile fatty acid production. Results: The results of the first stage showed that seven herbal plants (Moringa oleifera, Rhodomyrtus tomentosa, Clerodendron serratum, Curcuma longa Linn., Urena lobata, Uncaria, and Parkia timoriana) significantly differed in terms of total gas production (p < 0.05). Herbal plants can increase gas production and reduce protozoan populations. The highest total gas production was observed using P. timoriana, M. oleifera, and C. longa Linn. Moringa oleifera plants were the most effective in lowering protozoa population. In Stage 2, the supplementation of herbal plants in PKC-based-diet significantly increased IVDMD, that was ranged from 56.72% to 65.77%, IVOMD that was ranged from 52.10% to 59.54%, and NH3, that was ranged from 13.20 mM to 17.91 mM. Volatile fatty acid partial and total gas production potential and CH4 gas emissions were also significantly different from those of the control (p < 0.05). Conclusion: Supplementation of M. oleifera, C. longa Linn., and P. timoriana in ruminant diet effectively increased total gas production, IVDMD percentage, and IVOMD, and reduced CH4 gas emissions and protozoa populations during rumen fermentation.

Effects of rumen-degradable-to-undegradable protein ratio in ruminant diet on in vitro digestibility, rumen fermentation, and microbial protein synthesis.

BACKGROUND AND AIM: Feeding ruminants must notice the degradability of feed, especially protein. Microbial rumen requires ammonia from rumen degradable protein (RDP) beside that ruminant require bypass protein or rumen undegradable protein (RUP) and microbial crude protein. The aim of the study was to discover the best RDP:RUP ratio in beef cattle diets commonly used by Indonesian farmers using an in vitro methodology. MATERIALS AND METHODS: Samples of Pennisetum purpureum, Leucaena leucocephala, Indigofera zollingeriana, cassava, maize, palm kernel cake, rice bran, and tofu waste were formulated into dietary treatments (dry matter [DM] basis). All experiments were carried out using a 3×3×2 factorial, randomized block design with three replications. Treatments consisted of three protein levels (12%, 14%, and 16%), two energy levels (65% and 70%), and three RDP:RUP ratio levels (55:45, 60:40, and 65:35). The experimental diets were incubated in vitro using buffered rumen fluid for 48 h at 39°C. After incubation, the supernatants were analyzed to determine pH, ammonia concentration, total volatile fatty acid (VFA), and microbial protein synthesis. The residues were analyzed to determine DM, organic matter, protein, and RUP digestibility. RESULTS: Increased protein, energy, and RDP levels increased digestibility, ammonia concentrations, total VFAs, and microbial protein synthesis (p<0.05), while rations with 16% protein lowered these parameters (p<0.05). CONCLUSION: Increased dietary protein (from 12% to 14% DM), energy (from 65% to 70% DM), and RDP (from 55% to 65% crude protein [CP]) levels increased nutrient digestibility, ammonia concentration, total VFA levels, and microbial protein synthesis. The diet containing 14% DM dietary protein and 70% DM energy, which contained 55%, 60%, or 65% CP RDP optimally increased nutrient digestibility, ammonia concentration, total VFA levels, and microbial protein synthesis. Thus, feed based on these RDP:RUP ratios can optimize ruminant productivity.

In vitro evaluation of ruminant feed from West Sumatera based on chemical composition and content of rumen degradable and rumen undegradable proteins.

AIM: This research aimed to discover the chemical composition, as well as the content of the degradable and undegradable protein of the ruminant feed commonly used as cattle feed by Indonesian farmers. MATERIALS AND METHODS: In this study, Pennisetum purpureum, Leucaena leucocephala, Indigofera zollingeriana, Gliricidia sepium, cassava, maize, palm kernel cake, and rice bran were used as feed. Chemical composition was determined by proximate and Van Soest analyses performed in triplicate. Dry matter and organic matter digestibility, as well as the rumen degradable proteins (RDP) and rumen undegradable proteins (RUP) contents, were determined in vitro using the Tilley and Terry method. RESULTS: The results showed that more proteins can be obtained from legumes than from grass or concentrates. The highest protein amount was obtained from I. zollingerian (31.22%), while the lowest protein amount was obtained from cassava (3.59%). Dry matter digestibility ranged from 18.53% (rice bran) to 49.21% (G. sepium). Organic matter digestibility ranged from 35.71% (cassava) to 59.57% (I. zollingerian). Rice bran had the highest RDP from concentrate (73.26%), whereas I. zollingerian had the highest RDP from forage (74.72%). The highest RUP from concentrate was obtained from palm kernel cake (61.01%), and the highest RUP from forage was obtained from L. leucocephala (49.23%). CONCLUSION: The preparation of ruminant livestock rations must be based on RDP and RUP to meet the needs of both the rumen microbes and host animals. Information regarding the RDP and RUP of feeds is still limited, making this study useful in the preparation of ruminant livestock rations based on RDP and RUP ratios.

In vitro rumen biohydrogenation of unsaturated fatty acids in tropical grass-legume rations.

AIM: The aim of this study was to evaluate the effects of various combinations of tropical grass-legume species in rations on the biohydrogenation (BH) activity of unsaturated fatty acids (FAs), C18:0 composition, and fermentation profile in an in vitro rumen system. MATERIALS AND METHODS: Samples of the following five fodder plants were used: One species of grass (Pennisetum purpureum) and four species of tree legumes (Leucaena leucocephala, Gliricidia sepium, Calliandra calothyrsus, and Indigofera zollingeriana). The following eight experimental diets were evaluated: 50% P. purpureum + 50% L. leucocephala (LL I); 50% P. purpureum + 50% G. sepium (GS I); 50% P. purpureum + 50% C. calothyrsus (CC I); 50% P. purpureum + 50% I. zollingeriana (IZ I); 75% P. purpureum + 25% L. leucocephala (LL II); 75% P. purpureum + 25% G. sepium (GS II); 75% P. purpureum + 25% C. calothyrsus (CC II); and 75% P. purpureum + 25% I. zollingeriana (IZ II). Each ration was replicated 3 times. In vitro rumen incubation was performed for 48 h, according to the Tilley and Terry method. Determination of the FA profiles of the forage materials and rumen fluid samples was performed using gas chromatography. RESULTS: The percentage of polyunsaturated FA (PUFA) in the forage materials ranged from 34.18% (P. purpureum) to 74.51% (C. calothyrsus). The percentage of monounsaturated FA (MUFA) ranged from 5.06% (P. purpureum) to 8.71% (L. leucocephala). The percentage of saturated FA (SFA) was the lowest at 19.12% (C. calothyrsus) and highest at 60.76% (P. purpureum). In vitro BH of C18:3 n-3, C18:2 n-6, C18:1 n-9, and C18 PUFA in the experimental diets ranged from 72% to 100%. The BH of C18:1 n-9 in GS I (80%) and IZ I (72%) was significantly different (p<0.05). The percentage of C18:0 was 10-50% and significantly different (p<0.05) among treatments, with the highest (of 50%) in GS II. No significant differences (p>0.05) were observed in the fermentation parameters (pH, total volatile FAs, in vitro dry matter digestibility, and in vitro organic matter digestibility) among the treatments, except in NH3 concentration (p<0.05). CONCLUSION: The various combinations of tropical legumes do not have significant inhibitory effects on the BH of C18:2 n-6, C18:3 n-3, and C18 PUFA after in vitro incubation for 48h. Furthermore, an increase in the tropical legume ratio in the ration tends to suppress C18:0 formation after the fermentation simulation process. IZ I has the potential to reduce C18:1 n-9 (MUFA) disappearance and yield an ideal rumen fermentation profile.